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- PDB-4rao: Aza-acyclic nucleoside phosphonates containing a second phosphona... -

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Basic information

Entry
Database: PDB / ID: 4rao
TitleAza-acyclic nucleoside phosphonates containing a second phosphonate group as inhibitors of the human, Plasmodium falciparum and vivax 6-oxopurine phosphoribosyltransferases and their pro-drugs as antimalarial agents
ComponentsHypoxanthine-guanine phosphoribosyltransferase
KeywordsTRANSFERASE/TRANSFERASE INHIBITOR / 6-oxopurine phosphoribosyltransferase / 9-[(N-Phosphonoethyl-N-phosphonoethoxyethyl)-2-aminoethyl]hypoxanthine / cytoplasmic / TRANSFERASE-TRANSFERASE INHIBITOR complex
Function / homology
Function and homology information


adenine metabolic process / Defective HPRT1 disrupts guanine and hypoxanthine salvage / GMP catabolic process / guanine salvage / hypoxanthine metabolic process / hypoxanthine salvage / cerebral cortex neuron differentiation / positive regulation of dopamine metabolic process / lymphocyte proliferation / hypoxanthine phosphoribosyltransferase ...adenine metabolic process / Defective HPRT1 disrupts guanine and hypoxanthine salvage / GMP catabolic process / guanine salvage / hypoxanthine metabolic process / hypoxanthine salvage / cerebral cortex neuron differentiation / positive regulation of dopamine metabolic process / lymphocyte proliferation / hypoxanthine phosphoribosyltransferase / IMP metabolic process / GMP salvage / guanine phosphoribosyltransferase activity / hypoxanthine phosphoribosyltransferase activity / grooming behavior / IMP salvage / Purine salvage / striatum development / AMP salvage / dopaminergic neuron differentiation / purine nucleotide biosynthetic process / Azathioprine ADME / purine ribonucleoside salvage / dendrite morphogenesis / dopamine metabolic process / central nervous system neuron development / response to amphetamine / locomotory behavior / T cell mediated cytotoxicity / protein homotetramerization / nucleotide binding / magnesium ion binding / extracellular exosome / identical protein binding / cytosol / cytoplasm
Similarity search - Function
Hypoxanthine phosphoribosyl transferase / Purine/pyrimidine phosphoribosyl transferases signature. / Rossmann fold - #2020 / Phosphoribosyl transferase domain / Phosphoribosyltransferase-like / Phosphoribosyltransferase domain / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-3L7 / Hypoxanthine-guanine phosphoribosyltransferase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.871 Å
AuthorsKeough, D.T. / Hockova, D. / Janeba, Z. / Wang, T.-H. / Naesens, L. / Edstein, M.D. / Chavchich, M. / Guddat, L.W.
CitationJournal: J.Med.Chem. / Year: 2015
Title: Aza-acyclic Nucleoside Phosphonates Containing a Second Phosphonate Group As Inhibitors of the Human, Plasmodium falciparum and vivax 6-Oxopurine Phosphoribosyltransferases and Their Prodrugs ...Title: Aza-acyclic Nucleoside Phosphonates Containing a Second Phosphonate Group As Inhibitors of the Human, Plasmodium falciparum and vivax 6-Oxopurine Phosphoribosyltransferases and Their Prodrugs As Antimalarial Agents.
Authors: Keough, D.T. / Hockova, D. / Janeba, Z. / Wang, T.H. / Naesens, L. / Edstein, M.D. / Chavchich, M. / Guddat, L.W.
History
DepositionSep 10, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 7, 2015Provider: repository / Type: Initial release
Revision 1.1Feb 11, 2015Group: Database references
Revision 1.2Dec 23, 2015Group: Structure summary
Revision 1.3Jan 24, 2018Group: Structure summary / Category: audit_author / Item: _audit_author.name
Revision 1.4Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_alt_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_alt_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Hypoxanthine-guanine phosphoribosyltransferase
B: Hypoxanthine-guanine phosphoribosyltransferase
C: Hypoxanthine-guanine phosphoribosyltransferase
D: Hypoxanthine-guanine phosphoribosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)99,86816
Polymers97,9254
Non-polymers1,94412
Water3,621201
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11660 Å2
ΔGint-90 kcal/mol
Surface area29070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.602, 92.853, 114.849
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
Hypoxanthine-guanine phosphoribosyltransferase / / HGPRT / HGPRTase


Mass: 24481.217 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HPRT1, HPRT / Production host: Escherichia coli (E. coli)
References: UniProt: P00492, hypoxanthine phosphoribosyltransferase
#2: Chemical
ChemComp-3L7 / (2-{[2-(6-oxo-1,6-dihydro-9H-purin-9-yl)ethyl](2-{[(E)-2-phosphonoethenyl]oxy}ethyl)amino}ethyl)phosphonic acid


Mass: 437.282 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C13H21N5O8P2
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 201 / Source method: isolated from a natural source / Formula: H2O

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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: 2.09 Å3/Da / Density % sol: 41.02 %

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.95369 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Aug 5, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95369 Å / Relative weight: 1
ReflectionResolution: 1.87→46.43 Å / Num. obs: 68208 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASESphasing
PHENIX(phenix.refine: 1.8.2_1309)refinement
XDSdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.871→35.407 Å / SU ML: 0.19 / σ(F): 1.34 / Phase error: 23.44 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflectionSelection details
Rfree0.2302 2000 2.94 %Random
Rwork0.201 ---
obs0.2019 68117 99.78 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.871→35.407 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6361 0 120 201 6682
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0076832
X-RAY DIFFRACTIONf_angle_d1.2229287
X-RAY DIFFRACTIONf_dihedral_angle_d15.8532652
X-RAY DIFFRACTIONf_chiral_restr0.0781037
X-RAY DIFFRACTIONf_plane_restr0.0041170
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.871-1.91760.2811400.26234631X-RAY DIFFRACTION99
1.9176-1.96940.25751410.2364669X-RAY DIFFRACTION100
1.9694-2.02730.26471410.22954654X-RAY DIFFRACTION100
2.0273-2.09280.28561410.23524653X-RAY DIFFRACTION100
2.0928-2.16760.2731420.21684710X-RAY DIFFRACTION100
2.1676-2.25430.28261420.22354694X-RAY DIFFRACTION100
2.2543-2.35690.25281420.22534684X-RAY DIFFRACTION100
2.3569-2.48110.26451430.21914713X-RAY DIFFRACTION100
2.4811-2.63650.2281420.22334727X-RAY DIFFRACTION100
2.6365-2.840.25021430.22554706X-RAY DIFFRACTION100
2.84-3.12570.25821430.21164737X-RAY DIFFRACTION100
3.1257-3.57760.22311450.19534767X-RAY DIFFRACTION100
3.5776-4.5060.17631460.16154836X-RAY DIFFRACTION100
4.506-35.41340.20571490.18074936X-RAY DIFFRACTION99
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)
15.9643-1.19051.02964.4104-1.21361.80460.35930.5049-0.0274-0.229-0.3701-0.29740.06520.6322-0.0160.2761-0.03310.05130.3888-0.05460.191418.47222.5508-3.4232
26.3478-1.6751-1.33689.32512.91915.48940.13740.47520.8809-0.22520.0174-0.9703-1.48780.5679-0.10240.5345-0.11460.01310.3390.07110.273215.57415.0112-2.1731
31.82291.08990.25873.0929-0.00752.87580.1555-0.07810.01650.1337-0.12020.04580.06270.1012-0.03990.19210.00570.00410.2423-0.01430.179312.0299-4.869213.7308
49.37396.79260.78144.9720.40670.0627-0.10870.0667-0.3674-0.41850.1934-0.1040.01790.2954-0.09510.4573-0.03630.01540.3327-0.02290.271510.8742-4.696622.3544
52.97740.28342.31893.5114-2.36318.1942-0.03850.09950.16320.0202-0.0321-0.32840.03880.41880.08120.2424-0.0124-0.03840.303-0.05670.15725.3619-1.190321.8612
62.0134-0.43470.05313.7565-0.85143.64920.08970.01770.28390.0164-0.1132-0.6065-0.37360.72210.06330.255-0.09860.01890.4224-0.02210.282723.16936.26827.3597
73.62871.04840.34723.1423-1.04463.00070.0960.3007-0.3171-0.1329-0.0124-0.37550.14120.4958-0.05390.20250.04810.03640.3236-0.06470.25511.7905-9.319-7.9593
83.0545-4.06012.77276.2816-2.87397.7011-0.0759-0.09910.3418-0.04250.280.2201-0.6067-0.3073-0.11970.2348-0.0059-0.00910.21470.04690.27390.1629.1215-7.3183
92.29390.4367-0.19083.18530.97224.5097-0.05910.09890.3597-0.1435-0.00410.565-0.4725-0.0689-0.00090.19760.0082-0.03070.18060.03450.2866-9.07215.0697-6.7935
104.708-0.28970.54546.55432.92299.01360.01670.18320.63990.1989-0.16560.1336-0.4471-0.29820.02860.32850.0033-0.07560.28090.08190.4418-13.62015.4722-8.73
115.6249-2.4673-1.02654.2114-1.03214.75360.30660.149-0.31290.31230.33311.87420.5098-1.0567-0.47210.4451-0.0544-0.17370.5360.07580.702-19.45811.0517-17.8888
127.4033-3.0711-0.19553.3607-0.24943.19280.04490.2226-0.2503-0.47130.04330.6805-0.16520.0517-0.08990.3105-0.0078-0.12920.20460.05760.2996-8.02892.8212-20.8366
131.8428-2.1537-1.84383.48671.49012.6575-0.11210.29520.1938-0.12340.11840.0988-0.1890.07460.04740.302-0.0475-0.0280.28420.04840.21831.72173.5405-22.9572
143.62591.7450.33826.645-0.84313.8025-0.0850.4215-0.4131-0.48850.1456-0.04320.54450.0073-0.07110.26740.02610.00260.286-0.07120.23423.7454-13.7514-12.7741
152.4939-0.7858-1.21060.27160.15074.03670.2196-0.1074-0.37311.2339-0.64451.0583-0.1297-0.69320.30670.4519-0.11230.2360.5025-0.15210.5261-14.80025.264125.7419
164.59581.4541.94882.08550.09795.31450.4184-0.3626-0.5220.4671-0.13810.16030.6002-0.2884-0.27720.4199-0.11740.04040.29990.03250.3372-6.2078-8.01425.2309
175.79324.20640.09056.3044-0.06633.87630.10310.06240.7132-0.54210.09490.1644-0.6505-0.1254-0.10660.34-0.00010.12240.2063-0.02350.3313-4.535414.347413.8291
184.6491-0.66651.34980.53650.87483.0010.05770.03390.42250.0477-0.10150.1085-0.5330.30550.02320.3351-0.10630.08090.2157-0.03420.2646.002713.86915.5492
193.76622.5060.27963.80533.06113.8671-0.3232-0.03180.7002-0.24470.11260.27-1.6107-0.10090.32920.5092-0.07120.0850.3385-0.04470.46549.000217.307112.2154
205.1569-2.98253.67733.0106-4.6969.63580.2981-0.3220.72130.1061-0.8327-1.29780.49721.05130.34720.5071-0.04570.11610.47350.03980.534116.285821.230825.168
215.70292.4706-2.02667.0638-2.92628.3276-0.0218-0.40650.15860.2687-0.3832-0.2002-0.04490.08730.38420.2659-0.03450.06770.2222-0.05940.26175.628619.918529.9169
227.22224.8860.03287.6794-0.28472.90070.00940.36120.28290.04560.0181-0.0041-0.3718-0.19610.02420.3617-0.06790.13590.2-0.07040.30011.994720.892424.2281
230.28010.3319-1.22570.4819-1.63676.00050.3794-0.58280.40050.605-0.09970.3705-1.4104-0.1493-0.31740.5744-0.07770.22310.489-0.13190.4615-5.643917.676131.3303
246.1945-2.51231.4515.2026-1.77822.89290.0302-0.584-0.03940.7396-0.0750.0436-0.18880.25720.04320.3827-0.12380.06930.3258-0.01950.2227-1.28432.649230.3826
256.5854-0.9788-0.01217.0219-1.64773.84710.2853-1.1363-0.3380.7591-0.0161-0.1311-0.16040.0951-0.26640.3256-0.11660.02920.34940.02290.243-0.2277-4.958931.0597
262.01541.57590.64821.47061.66844.93270.2635-0.19580.36660.2279-0.20620.6715-0.6958-0.4394-0.11520.29380.06280.10.3022-0.04110.5025-19.76877.926212.3306
272.6384-0.40530.04980.73630.91043.0040.0868-0.0227-0.21570.08340.01410.1540.17250.173-0.09010.2029-0.0174-0.01110.16820.00180.2818-9.318-11.1194.896
285.87113.21493.39772.53531.66866.10680.0517-0.1318-0.38110.0170.11040.04160.2354-0.226-0.21150.2033-0.0290.03660.2437-0.00460.2731-7.3858-15.3306-2.4011
295.8089-4.92884.06934.6034-4.68915.80750.14870.72540.6893-1.1507-0.5453-0.65190.33560.00480.48850.405-0.091-0.05580.433-0.05590.4386-21.1679-17.6624-10.5807
303.1201-2.9147-2.08557.17024.80933.90620.01710.17050.0210.1975-0.13440.10690.1501-0.24350.12380.1555-0.0535-0.00140.17990.03250.253-22.0224-16.95230.6254
311.13350.5127-0.48593.0594-0.3463.50830.04160.18680.20850.0127-0.03630.6115-0.3381-0.6544-0.01060.22280.06580.01590.3741-0.00670.4971-24.67840.88135.0001
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 24 )
2X-RAY DIFFRACTION2chain 'A' and (resid 25 through 37 )
3X-RAY DIFFRACTION3chain 'A' and (resid 38 through 86 )
4X-RAY DIFFRACTION4chain 'A' and (resid 87 through 100 )
5X-RAY DIFFRACTION5chain 'A' and (resid 101 through 152 )
6X-RAY DIFFRACTION6chain 'A' and (resid 153 through 216 )
7X-RAY DIFFRACTION7chain 'B' and (resid 4 through 37 )
8X-RAY DIFFRACTION8chain 'B' and (resid 38 through 56 )
9X-RAY DIFFRACTION9chain 'B' and (resid 57 through 87 )
10X-RAY DIFFRACTION10chain 'B' and (resid 88 through 100 )
11X-RAY DIFFRACTION11chain 'B' and (resid 101 through 127 )
12X-RAY DIFFRACTION12chain 'B' and (resid 128 through 165 )
13X-RAY DIFFRACTION13chain 'B' and (resid 166 through 179 )
14X-RAY DIFFRACTION14chain 'B' and (resid 180 through 217 )
15X-RAY DIFFRACTION15chain 'C' and (resid 4 through 17 )
16X-RAY DIFFRACTION16chain 'C' and (resid 18 through 37 )
17X-RAY DIFFRACTION17chain 'C' and (resid 38 through 56 )
18X-RAY DIFFRACTION18chain 'C' and (resid 57 through 85 )
19X-RAY DIFFRACTION19chain 'C' and (resid 86 through 100 )
20X-RAY DIFFRACTION20chain 'C' and (resid 101 through 127 )
21X-RAY DIFFRACTION21chain 'C' and (resid 128 through 152 )
22X-RAY DIFFRACTION22chain 'C' and (resid 153 through 165 )
23X-RAY DIFFRACTION23chain 'C' and (resid 166 through 179 )
24X-RAY DIFFRACTION24chain 'C' and (resid 180 through 197 )
25X-RAY DIFFRACTION25chain 'C' and (resid 198 through 217 )
26X-RAY DIFFRACTION26chain 'D' and (resid 4 through 37 )
27X-RAY DIFFRACTION27chain 'D' and (resid 38 through 85 )
28X-RAY DIFFRACTION28chain 'D' and (resid 86 through 102 )
29X-RAY DIFFRACTION29chain 'D' and (resid 103 through 127 )
30X-RAY DIFFRACTION30chain 'D' and (resid 128 through 165 )
31X-RAY DIFFRACTION31chain 'D' and (resid 166 through 217 )

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