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- PDB-7kyy: Crystal structure of Plasmodium falciparum dihydroorotate dehydro... -

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Basic information

Entry
Database: PDB / ID: 7kyy
TitleCrystal structure of Plasmodium falciparum dihydroorotate dehydrogenase bound with Inhibitor DSM697 (3-methyl-N-(1-(5-methylisoxazol-3-yl)ethyl)-4-(6-(trifluoromethyl)-1H-indol-3-yl)-1H-pyrrole-2-carboxamide)
ComponentsDihydroorotate dehydrogenase (quinone), mitochondrial
KeywordsOXIDOREDUCTASE/OXIDOREDUCTASE INHIBITOR / Alpha-Beta Barrel / OXIDOREDUCTASE / OXIDOREDUCTASE-OXIDOREDUCTASE INHIBITOR complex
Function / homology
Function and homology information


Pyrimidine biosynthesis / pyrimidine ribonucleotide biosynthetic process / dihydroorotate dehydrogenase (quinone) / dihydroorotate dehydrogenase (quinone) activity / dihydroorotate dehydrogenase activity / 'de novo' UMP biosynthetic process / 'de novo' pyrimidine nucleobase biosynthetic process / mitochondrial inner membrane
Similarity search - Function
Dihydroorotate dehydrogenase, class 2 / Dihydroorotate dehydrogenase signature 1. / Dihydroorotate dehydrogenase signature 2. / Dihydroorotate dehydrogenase, conserved site / : / Dihydroorotate dehydrogenase domain / Dihydroorotate dehydrogenase / Aldolase class I / Aldolase-type TIM barrel / TIM Barrel ...Dihydroorotate dehydrogenase, class 2 / Dihydroorotate dehydrogenase signature 1. / Dihydroorotate dehydrogenase signature 2. / Dihydroorotate dehydrogenase, conserved site / : / Dihydroorotate dehydrogenase domain / Dihydroorotate dehydrogenase / Aldolase class I / Aldolase-type TIM barrel / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
FLAVIN MONONUCLEOTIDE / OROTIC ACID / Chem-XCD / Dihydroorotate dehydrogenase (quinone), mitochondrial
Similarity search - Component
Biological speciesPlasmodium falciparum (malaria parasite P. falciparum)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsDeng, X. / Phillips, M. / Tomchick, D.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01AI103947 United States
CitationJournal: J.Med.Chem. / Year: 2021
Title: Potent Antimalarials with Development Potential Identified by Structure-Guided Computational Optimization of a Pyrrole-Based Dihydroorotate Dehydrogenase Inhibitor Series.
Authors: Palmer, M.J. / Deng, X. / Watts, S. / Krilov, G. / Gerasyuto, A. / Kokkonda, S. / El Mazouni, F. / White, J. / White, K.L. / Striepen, J. / Bath, J. / Schindler, K.A. / Yeo, T. / ...Authors: Palmer, M.J. / Deng, X. / Watts, S. / Krilov, G. / Gerasyuto, A. / Kokkonda, S. / El Mazouni, F. / White, J. / White, K.L. / Striepen, J. / Bath, J. / Schindler, K.A. / Yeo, T. / Shackleford, D.M. / Mok, S. / Deni, I. / Lawong, A. / Huang, A. / Chen, G. / Wang, W. / Jayaseelan, J. / Katneni, K. / Patil, R. / Saunders, J. / Shahi, S.P. / Chittimalla, R. / Angulo-Barturen, I. / Jimenez-Diaz, M.B. / Wittlin, S. / Tumwebaze, P.K. / Rosenthal, P.J. / Cooper, R.A. / Aguiar, A.C.C. / Guido, R.V.C. / Pereira, D.B. / Mittal, N. / Winzeler, E.A. / Tomchick, D.R. / Laleu, B. / Burrows, J.N. / Rathod, P.K. / Fidock, D.A. / Charman, S.A. / Phillips, M.A.
History
DepositionDec 9, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 19, 2021Provider: repository / Type: Initial release
Revision 1.1Dec 8, 2021Group: Database references / Category: citation / citation_author / database_2
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Dihydroorotate dehydrogenase (quinone), mitochondrial
B: Dihydroorotate dehydrogenase (quinone), mitochondrial
C: Dihydroorotate dehydrogenase (quinone), mitochondrial
D: Dihydroorotate dehydrogenase (quinone), mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)185,65916
Polymers181,5444
Non-polymers4,11512
Water8,755486
1
A: Dihydroorotate dehydrogenase (quinone), mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,4154
Polymers45,3861
Non-polymers1,0293
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Dihydroorotate dehydrogenase (quinone), mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,4154
Polymers45,3861
Non-polymers1,0293
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Dihydroorotate dehydrogenase (quinone), mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,4154
Polymers45,3861
Non-polymers1,0293
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Dihydroorotate dehydrogenase (quinone), mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,4154
Polymers45,3861
Non-polymers1,0293
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)93.061, 97.254, 186.882
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein
Dihydroorotate dehydrogenase (quinone), mitochondrial / DHOdehase / Dihydroorotate oxidase


Mass: 45385.914 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium falciparum (isolate 3D7) (eukaryote)
Strain: isolate 3D7 / Gene: PFF0160c / Plasmid: pET28b / Production host: Escherichia coli (E. coli) / Strain (production host): DE3
References: UniProt: Q08210, dihydroorotate dehydrogenase (quinone)
#2: Chemical
ChemComp-XCD / 3-methyl-N-[(1R)-1-(5-methyl-1,2-oxazol-3-yl)ethyl]-4-[6-(trifluoromethyl)-1H-indol-3-yl]-1H-pyrrole-2-carboxamide


Mass: 416.396 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H19F3N4O2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE


Mass: 456.344 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C17H21N4O9P / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-ORO / OROTIC ACID


Mass: 156.096 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C5H4N2O4 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 486 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.28 Å3/Da / Density % sol: 46.1 % / Description: prism
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 85 mM HEPES pH 7.5, 2-propanol 8.5%, 17% PEG 4000, 15% v/v Glycerol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97895 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 13, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97895 Å / Relative weight: 1
ReflectionResolution: 2→47.06 Å / Num. obs: 115187 / % possible obs: 99.7 % / Redundancy: 7.2 % / Biso Wilson estimate: 21.37 Å2 / Rpim(I) all: 0.044 / Net I/σ(I): 17.55
Reflection shellResolution: 2→2.03 Å / Redundancy: 6.5 % / Mean I/σ(I) obs: 1.43 / Num. unique obs: 5586 / Rpim(I) all: 0.542 / % possible all: 98.3

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3I65

3i65


Resolution: 2→47.06 Å / SU ML: 0.1785 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 19.7361
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2069 1008 1 %
Rwork0.1627 100166 -
obs0.1631 101174 87.68 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 30.65 Å2
Refinement stepCycle: LAST / Resolution: 2→47.06 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11749 0 288 486 12523
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.008412281
X-RAY DIFFRACTIONf_angle_d0.906216585
X-RAY DIFFRACTIONf_chiral_restr0.05051834
X-RAY DIFFRACTIONf_plane_restr0.00552092
X-RAY DIFFRACTIONf_dihedral_angle_d19.28264580
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.10.2352880.18038452X-RAY DIFFRACTION52.43
2.1-2.240.19531120.166911377X-RAY DIFFRACTION70.46
2.24-2.410.21431450.172614839X-RAY DIFFRACTION91.72
2.41-2.650.23771610.166616150X-RAY DIFFRACTION99.42
2.65-3.030.21821730.167416268X-RAY DIFFRACTION99.85
3.03-3.820.2011650.158516317X-RAY DIFFRACTION99.67
3.82-47.060.18991640.156416763X-RAY DIFFRACTION99.33
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
14.591473620580.745551585986-0.6910274296593.56336458785-0.4353805966985.034617056060.1326380381410.02064439414970.01793549175030.188561263041-0.0558522255441-0.288328698832-0.2533284500910.552593814799-0.13928599950.1317662691150.0169448681861-0.06248765845560.2815166602070.02309308707310.227580370089-7.925764226977.52535894895-10.2304409439
22.29554305857-0.1223494974160.3047301630221.708964307330.4934371872662.740476809030.000655833970882-0.207871379494-0.2387191617480.2277647293260.02824511252-0.07328469829620.314325309053-0.0262971540865-0.03564230638560.20436983234-0.0114815501722-0.01190949500760.1195255383240.04051844968170.113559246504-24.28366206781.07944996057-13.0858082834
32.438454366370.4354996489030.4750226321411.890044937210.05276310584892.421419514280.06584441757580.178005266286-0.1993655100670.02829948464570.0249960267376-0.07219290873970.2335684304570.0266102702118-0.04557194572050.149423122819-0.03051471384960.001770583433110.100617481024-0.007710247193940.0657296302645-29.9737555806-1.96918552667-24.6538039917
42.48333535184-0.2186739462960.453375944881.287556422410.3894781509452.4463714941-0.0928119083797-0.1150624087680.3842526197950.1316446394370.02378128749950.0208503798068-0.404080858481-0.07047976968710.02565473260650.209739264686-0.0156540502570.001509224228060.07674468005150.004941433045750.138446437251-30.993476964116.2247050714-16.878568957
54.442479795060.8369873250930.08386014897582.35634274582-0.5083215424571.10958204013-0.02509909466760.2367706768890.0765291862209-0.587258203912-0.145834911516-0.3067225399070.3496169041170.5812902932490.1636105684560.3402367720020.0423555367910.05143949833770.5152635816820.09648249387580.181318833359-6.04200942208-2.7569340844711.8524996119
61.90199220441-0.04371690834030.05587947102952.58402210984-0.3662772825192.127898217830.004012888616920.2881671072930.14698972546-0.196692100603-0.05748163527490.0701710771017-0.02787229881190.2282801104730.04248851150.1605223415640.0161858912144-0.03914697954790.1227347316510.03327085234820.0767772307896-21.8695785766-0.83282422696319.6017800715
72.5963003211-0.618338626356-0.05257794268992.23443206356-0.3309430773041.9381662162-0.02677622334920.04367490999870.3732074772910.0200853594074-0.0928566589231-0.283470218912-0.4521119032580.6092622165860.04043245397640.204909477414-0.134619901771-0.05848604655540.1973799255650.0654981817850.157211525838-13.62147930398.0976649542128.3870080768
82.8520047232-0.9312821898251.468586940754.67581330622-2.899099073255.52979996831-0.320921850963-0.4984607502360.5006057528730.4236918979010.3263309992450.150609636022-0.823378879609-0.5370715227350.03208261023420.309250096712-0.000913668397566-0.01577664304060.153198921962-0.02818839460390.194855639473-27.150996742712.287781646139.7559101723
92.19019784946-0.193935023910.4890087106972.0750921082-0.9227024133062.90413801160.0108144695773-0.1735186784640.1158852789490.0822877793892-0.0003525193618090.114287818729-0.1622794875750.125382734358-0.04509208474740.122067800838-0.0305336482367-0.01384813468950.0795778072524-0.03930595576170.094176108223-25.30479504412.7050820553636.1743014221
105.7588368791-1.140557019960.2978468108532.10363854815-0.2118197494051.41824520552-0.269796692542-0.216596555975-0.5126012770470.581486206330.0276489297914-0.122208145740.1048637013630.654100650427-0.03541494643090.1096296386940.0568837630594-0.1350706188820.4012815365040.1011631461310.0821647650892-8.71775049628-6.5260225334836.2162741892
112.40200468239-0.158329970343-0.04757153734361.660092522230.03935054007931.85784023528-0.00390339844448-0.0729886987049-0.336782546784-0.0972043539361-0.1115601091920.04046084270370.2244178865180.3202826846540.09305386322190.1340506232330.0480150768314-0.03151575931630.1000024726360.02355989578760.0989904142912-18.5073256947-11.190925034530.0353441953
123.730195200292.02560030614-1.14396163363.96598115623-1.21371329152.13756737449-0.09146528438770.3396599759-0.245908141614-0.3994432594860.1216921090740.2958576389240.479067147311-0.04617155902550.01040031482560.196044367470.0322709094513-0.084952157830.102837674596-0.03057390685840.188554711874-26.7885175423-17.613475175920.7393809871
134.412665687820.267885447991-0.2298017604632.33841256587-0.364150545472.18125614674-0.0589274306622-0.0463539819745-0.322664697481-0.2077478927060.2600279150130.4685557478760.154958949304-0.523304298141-0.13993721480.198036907612-0.017738365434-0.07569365818190.2806298808880.06700673795860.300198836051-68.51851116784.799957758457.92821903594
142.53014462164-0.7819355819710.9407542394641.68728051470.1115534358242.15097290865-0.0209443959404-0.700098316728-0.3671858301540.3530408268140.2162193171740.4959009347650.14714266198-1.02373517533-0.305612636310.2536485022270.05533129145820.01214082913960.5648930604890.2032138188760.430365140515-71.73609912911.4674512285725.400087934
153.62168028054-0.05984677241541.695366936422.25269214684-0.6781412623144.334969498470.125744499379-0.590808602159-0.5353635662050.1111488820150.06333811538960.08023366502740.43069785974-0.265318426305-0.1043612340770.2558673876820.0141161105226-0.06940368756690.2499451326560.1162241594830.368010918245-55.2304838082-7.4583059707320.0956423011
163.8980400333-0.5837752503940.6195530619971.87082417778-0.4147054124451.24506940577-0.0228064726257-0.8844650300620.1424071301030.241188071840.1774708726250.0132264243952-0.213338147154-0.27573737959-0.1417971079020.2257181547760.104043053772-0.01677785215860.4269403598980.02132781868920.19590558395-55.92192499748.1141511110127.2427497201
172.243592266280.008350822800960.2441556144771.3723681695-0.7349373338282.8643189806-0.149388883653-0.2186160699630.3282873232890.08954364757930.1357961061340.0449670389322-0.44119041833-0.1562260485840.008919399131110.2217477648890.0599569332046-0.0475725787450.148664316395-0.03353666891530.258282670207-56.675723780316.908215432714.4828691111
182.67742227927-0.312101900218-4.315599060188.89427750516-1.430276047167.38497330720.246068498969-0.436276279461-0.04785220383221.24410539407-0.1905296711850.0915104861180.154506577370.2025632442-0.03946688702670.374738799911-0.05372216174090.06216766984150.509943262213-0.0588025458090.563169878225-84.7241624022-9.26027207918-10.1048564081
193.263752971840.21904287466-0.8495672403032.428953908550.314167796682.00023140410.001470900780320.7691282304550.29113956313-0.416821249052-0.08224379296160.202335648453-0.229305262097-0.5843791086470.06069291418790.1994672912610.067558887838-0.08838443248120.3028965151120.06350811815540.225248848862-70.2007363543-0.327929629708-30.5198503826
203.04767154893-0.746084074986-0.4427300232453.057439519810.5717383755981.74820309963-0.1720835500750.0214900502024-0.3131232102130.0864597783720.029796580208-0.02922456917740.245559499577-0.1126043132970.1337791870640.158045285883-0.05082249163760.005146773174990.0825080097594-0.02782648242360.266212825544-64.8366084298-16.8408520578-20.4928687417
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid -2 through 193 )AA-2 - 1931 - 38
22chain 'A' and (resid 194 through 262 )AA194 - 26239 - 107
33chain 'A' and (resid 263 through 474 )AA263 - 474108 - 283
44chain 'A' and (resid 475 through 567 )AA475 - 567284 - 376
55chain 'B' and (resid 167 through 205 )BE167 - 2051 - 39
66chain 'B' and (resid 206 through 247 )BE206 - 24740 - 83
77chain 'B' and (resid 248 through 356 )BE248 - 35684 - 192
88chain 'B' and (resid 357 through 376 )BE357 - 376193 - 212
99chain 'B' and (resid 377 through 448 )BE377 - 448213 - 250
1010chain 'B' and (resid 449 through 474 )BE449 - 474251 - 276
1111chain 'B' and (resid 475 through 537 )BE475 - 537277 - 339
1212chain 'B' and (resid 538 through 566 )BE538 - 566340 - 368
1313chain 'C' and (resid 160 through 247 )CI160 - 2471 - 91
1414chain 'C' and (resid 248 through 282 )CI248 - 28292 - 126
1515chain 'C' and (resid 283 through 418 )CI283 - 418127 - 226
1616chain 'C' and (resid 419 through 474 )CI419 - 474227 - 282
1717chain 'C' and (resid 475 through 567 )CI475 - 567283 - 377
1818chain 'D' and (resid 161 through 178 )DM161 - 1781 - 18
1919chain 'D' and (resid 179 through 528 )DM179 - 52819 - 335
2020chain 'D' and (resid 529 through 566 )DM529 - 566336 - 373

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Jul 12, 2017. Major update of PDB

Major update of PDB

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External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

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Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

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