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- PDB-6q13: CRYSTAL STRUCTURE OF LDHA IN COMPLEX WITH COMPOUND NCGC00420737-0... -

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Basic information

Entry
Database: PDB / ID: 6q13
TitleCRYSTAL STRUCTURE OF LDHA IN COMPLEX WITH COMPOUND NCGC00420737-09 AT 2.00 A RESOLUTION
ComponentsL-lactate dehydrogenase A chain
KeywordsOXIDOREDUCTASE/OXIDOREDUCTASE inhibitor / LDHA / OXIDOREDUCTASE-OXIDOREDUCTASE inhibitor complex
Function / homology
Function and homology information


oxidoreductase complex / Pyruvate metabolism / L-lactate dehydrogenase / lactate metabolic process / L-lactate dehydrogenase activity / pyruvate metabolic process / substantia nigra development / glycolytic process / cadherin binding / mitochondrion ...oxidoreductase complex / Pyruvate metabolism / L-lactate dehydrogenase / lactate metabolic process / L-lactate dehydrogenase activity / pyruvate metabolic process / substantia nigra development / glycolytic process / cadherin binding / mitochondrion / extracellular exosome / identical protein binding / membrane / nucleus / cytosol
Similarity search - Function
L-lactate dehydrogenase / L-lactate dehydrogenase active site. / L-lactate dehydrogenase, active site / L-lactate/malate dehydrogenase / Lactate/malate dehydrogenase, N-terminal / Lactate/malate dehydrogenase, C-terminal / lactate/malate dehydrogenase, NAD binding domain / lactate/malate dehydrogenase, alpha/beta C-terminal domain / Lactate dehydrogenase/glycoside hydrolase, family 4, C-terminal / NAD(P)-binding domain superfamily
Similarity search - Domain/homology
1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE / Chem-P8V / L-lactate dehydrogenase A chain
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsDavies, D.R. / Dranow, D.M.
CitationJournal: J.Med.Chem. / Year: 2020
Title: Pyrazole-Based Lactate Dehydrogenase Inhibitors with Optimized Cell Activity and Pharmacokinetic Properties.
Authors: Rai, G. / Urban, D.J. / Mott, B.T. / Hu, X. / Yang, S.M. / Benavides, G.A. / Johnson, M.S. / Squadrito, G.L. / Brimacombe, K.R. / Lee, T.D. / Cheff, D.M. / Zhu, H. / Henderson, M.J. / ...Authors: Rai, G. / Urban, D.J. / Mott, B.T. / Hu, X. / Yang, S.M. / Benavides, G.A. / Johnson, M.S. / Squadrito, G.L. / Brimacombe, K.R. / Lee, T.D. / Cheff, D.M. / Zhu, H. / Henderson, M.J. / Pohida, K. / Sulikowski, G.A. / Dranow, D.M. / Kabir, M. / Shah, P. / Padilha, E. / Tao, D. / Fang, Y. / Christov, P.P. / Kim, K. / Jana, S. / Muttil, P. / Anderson, T. / Kunda, N.K. / Hathaway, H.J. / Kusewitt, D.F. / Oshima, N. / Cherukuri, M. / Davies, D.R. / Norenberg, J.P. / Sklar, L.A. / Moore, W.J. / Dang, C.V. / Stott, G.M. / Neckers, L. / Flint, A.J. / Darley-Usmar, V.M. / Simeonov, A. / Waterson, A.G. / Jadhav, A. / Hall, M.D. / Maloney, D.J.
History
DepositionAug 2, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 23, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 7, 2020Group: Database references / Category: citation / citation_author
Item: _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Oct 21, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.3Oct 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: L-lactate dehydrogenase A chain
B: L-lactate dehydrogenase A chain
C: L-lactate dehydrogenase A chain
D: L-lactate dehydrogenase A chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)153,00026
Polymers146,9394
Non-polymers6,06222
Water17,312961
1
A: L-lactate dehydrogenase A chain
C: L-lactate dehydrogenase A chain
hetero molecules

A: L-lactate dehydrogenase A chain
C: L-lactate dehydrogenase A chain
hetero molecules


  • defined by author&software
  • Evidence: The biological assembly is a tetramer. MR placed subunits in a non-continuous manner. I was not able to create a compact continuous tetramer in the ASU for these coordinates. Can the ...Evidence: The biological assembly is a tetramer. MR placed subunits in a non-continuous manner. I was not able to create a compact continuous tetramer in the ASU for these coordinates. Can the annotator help with this so that a biological assembly is deposited as the coordinates set? Thanks
  • 153 kDa, 4 polymers
  • Search similar-shape structures of this assembly by Omokage search (details)
Theoretical massNumber of molelcules
Total (without water)153,12528
Polymers146,9394
Non-polymers6,18624
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-x,-y+1,z1
Buried area28830 Å2
ΔGint-132 kcal/mol
Surface area42420 Å2
MethodPISA
2
D: L-lactate dehydrogenase A chain
hetero molecules

D: L-lactate dehydrogenase A chain
hetero molecules

B: L-lactate dehydrogenase A chain
hetero molecules

B: L-lactate dehydrogenase A chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)152,87624
Polymers146,9394
Non-polymers5,93820
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_455-x-1,-y,z1
crystal symmetry operation3_445-x-1/2,y-1/2,-z1
crystal symmetry operation4_455x-1/2,-y+1/2,-z1
Buried area28480 Å2
ΔGint-131 kcal/mol
Surface area41860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)134.800, 94.740, 121.560
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11B-706-

HOH

21C-616-

HOH

31D-689-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 1 through 54 or resid 56...
21(chain B and (resid 1 through 13 or (resid 14...
31(chain C and (resid 1 through 13 or (resid 14...
41(chain D and (resid 1 through 13 or (resid 14...

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ALAALAGLUGLU(chain A and (resid 1 through 54 or resid 56...AA1 - 542 - 55
12LYSLYSPROPRO(chain A and (resid 1 through 54 or resid 56...AA56 - 7457 - 75
13LYSLYSLYSLYS(chain A and (resid 1 through 54 or resid 56...AA7576
14ALAALAPHEPHE(chain A and (resid 1 through 54 or resid 56...AA1 - 3312 - 332
15ALAALAPHEPHE(chain A and (resid 1 through 54 or resid 56...AA1 - 3312 - 332
16ALAALAPHEPHE(chain A and (resid 1 through 54 or resid 56...AA1 - 3312 - 332
17ALAALAPHEPHE(chain A and (resid 1 through 54 or resid 56...AA1 - 3312 - 332
21ALAALALYSLYS(chain B and (resid 1 through 13 or (resid 14...BB1 - 132 - 14
22GLUGLUGLNGLN(chain B and (resid 1 through 13 or (resid 14...BB14 - 1615 - 17
23ALAALAPHEPHE(chain B and (resid 1 through 13 or (resid 14...BB1 - 3312 - 332
24ALAALAPHEPHE(chain B and (resid 1 through 13 or (resid 14...BB1 - 3312 - 332
25ALAALAPHEPHE(chain B and (resid 1 through 13 or (resid 14...BB1 - 3312 - 332
26ALAALAPHEPHE(chain B and (resid 1 through 13 or (resid 14...BB1 - 3312 - 332
31ALAALALYSLYS(chain C and (resid 1 through 13 or (resid 14...CC1 - 132 - 14
32GLUGLUGLNGLN(chain C and (resid 1 through 13 or (resid 14...CC14 - 1615 - 17
33ALAALAPHEPHE(chain C and (resid 1 through 13 or (resid 14...CC1 - 3312 - 332
34ALAALAPHEPHE(chain C and (resid 1 through 13 or (resid 14...CC1 - 3312 - 332
35ALAALAPHEPHE(chain C and (resid 1 through 13 or (resid 14...CC1 - 3312 - 332
36ALAALAPHEPHE(chain C and (resid 1 through 13 or (resid 14...CC1 - 3312 - 332
41ALAALALYSLYS(chain D and (resid 1 through 13 or (resid 14...DD1 - 132 - 14
42GLUGLUGLNGLN(chain D and (resid 1 through 13 or (resid 14...DD14 - 1615 - 17
43ALAALAPHEPHE(chain D and (resid 1 through 13 or (resid 14...DD1 - 3312 - 332
44ALAALAPHEPHE(chain D and (resid 1 through 13 or (resid 14...DD1 - 3312 - 332
45ALAALAPHEPHE(chain D and (resid 1 through 13 or (resid 14...DD1 - 3312 - 332
46ALAALAPHEPHE(chain D and (resid 1 through 13 or (resid 14...DD1 - 3312 - 332

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Components

#1: Protein
L-lactate dehydrogenase A chain / LDH-A / Cell proliferation-inducing gene 19 protein / LDH muscle subunit / LDH-M / Renal carcinoma ...LDH-A / Cell proliferation-inducing gene 19 protein / LDH muscle subunit / LDH-M / Renal carcinoma antigen NY-REN-59


Mass: 36734.672 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: LDHA, PIG19 / Production host: Escherichia coli (E. coli) / References: UniProt: P00338, L-lactate dehydrogenase
#2: Chemical
ChemComp-NAI / 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE / NADH


Mass: 665.441 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H29N7O14P2
#3: Chemical
ChemComp-P8V / 2-[5-(cyclopropylmethyl)-4-[(3-fluoro-4-sulfamoylphenyl)methyl]-3-{3-[(5-methylthiophen-2-yl)ethynyl]phenyl}-1H-pyrazol-1-yl]-1,3-thiazole-4-carboxylic acid


Mass: 632.748 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C31H25FN4O4S3 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 961 / 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: 2.64 Å3/Da / Density % sol: 53.43 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 10% (W/V) PEG 8000, 100 MM IMIDAZOLE (PH 8.0); 25% EG CRYOPROTECTANT

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97856 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Nov 5, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 104626 / % possible obs: 99.1 % / Redundancy: 5.84 % / Biso Wilson estimate: 24.88 Å2 / Rmerge(I) obs: 0.073 / Net I/σ(I): 19.02
Reflection shellResolution: 2→2.05 Å / Rmerge(I) obs: 0.573 / Mean I/σ(I) obs: 3.08 / Num. unique obs: 7750 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIX1.11.1_2575refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
XSCALEdata scaling
MoRDaphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5W8L

5w8l


Resolution: 2→45.14 Å / SU ML: 0.21 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 20.76
RfactorNum. reflection% reflection
Rfree0.209 1916 1.83 %
Rwork0.169 --
obs-104552 99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 100.37 Å2 / Biso mean: 32.2992 Å2 / Biso min: 11.84 Å2
Refinement stepCycle: final / Resolution: 2→45.14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10068 0 404 979 11451
Biso mean--33.24 37.45 -
Num. residues----1324
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00710721
X-RAY DIFFRACTIONf_angle_d0.92714594
X-RAY DIFFRACTIONf_chiral_restr0.0561697
X-RAY DIFFRACTIONf_plane_restr0.0061805
X-RAY DIFFRACTIONf_dihedral_angle_d16.2656310
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A5938X-RAY DIFFRACTION7.596TORSIONAL
12B5938X-RAY DIFFRACTION7.596TORSIONAL
13C5938X-RAY DIFFRACTION7.596TORSIONAL
14D5938X-RAY DIFFRACTION7.596TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2-2.050.28331440.23887313100
2.05-2.10540.28521250.22657327100
2.1054-2.16730.23011380.2117292100
2.1673-2.23730.27611440.20637274100
2.2373-2.31720.22411280.20357325100
2.3172-2.410.23431370.19577337100
2.41-2.51970.28051300.18447317100
2.5197-2.65250.20091370.1771733799
2.6525-2.81870.21681380.1704730999
2.8187-3.03630.19891450.1685731599
3.0363-3.34170.21811360.1614731999
3.3417-3.82510.1761310.1511737099
3.8251-4.81830.16181630.1321738498
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)
10.5034-0.1631-0.47041.5172-0.67780.9077-0.21510.25240.0495-0.17340.1635-0.270.05950.15890.04920.2617-0.20340.03140.4938-0.03910.2329-47.1413-0.139-27.9828
20.5681-0.1052-0.41770.3744-0.01160.4164-0.20360.26310.1703-0.10510.1626-0.0038-0.12050.01150.03470.2532-0.1732-0.07970.40420.06620.2607-53.893420.4621-20.4129
31.26570.3379-0.26261.30590.53560.6009-0.1380.2534-0.0792-0.16020.07850.04750.0063-0.02030.05660.3478-0.3608-0.05670.59010.06830.3462-43.527528.7564-30.7778
46.7471-2.55192.3150.9975-0.69711.7308-0.1967-0.971-0.36220.41450.17280.06940.04890.17770.07120.3512-0.0325-0.05880.24060.03090.332219.499638.7745-27.4019
51.9005-0.6179-1.01190.8473-0.19892.0680.0036-0.1003-0.2394-0.0541-0.01320.14510.2061-0.0423-0.02250.2132-0.0374-0.03730.10370.0150.1704-6.585728.1895-33.4033
60.5299-0.1374-0.04390.9434-0.47980.90090.05190.0065-0.0162-0.1969-0.01020.17160.0623-0.1988-0.04770.1966-0.029-0.04950.1626-0.0110.1837-23.762641.3636-40.7321
71.543-2.11871.49357.0554-5.00975.41990.0171-0.161-0.22740.110.02640.15330.1323-0.3589-0.09530.1896-0.1042-0.05630.33540.0220.2793-34.87734.078-30.1321
80.1055-0.70880.30534.8833-1.71031.9591-0.01190.1088-0.0128-0.84420.00140.8591-0.1538-0.13070.02520.1835-0.0136-0.06230.32030.03720.3452-2.963368.3051-5.7868
90.3764-0.01540.35911.82030.82551.3487-0.0993-0.1360.0194-0.03690.0430.2316-0.0659-0.20720.04840.11440.036-0.01180.26720.02270.1789-20.145446.108-0.0077
100.8595-0.17060.29750.6174-0.16380.8731-0.147-0.2205-0.22390.05490.11210.08640.1538-0.07190.03460.1610.04240.06550.24920.06440.2189-12.061926.13787.6027
117.5112-3.25924.62215.9981-3.63639.6383-0.04470.1857-0.1905-0.2302-0.06930.38780.1532-0.13050.10840.259-0.08010.02020.19750.02540.3696-22.35417.2521-2.7735
122.4858-0.7941.69190.5459-0.70621.24410.42320.7472-0.1246-0.4739-0.24730.04450.232-0.0273-0.14890.73510.0882-0.21040.30650.04540.3148-20.685951.2006-67.5223
131.4525-0.7131-0.98030.62790.70281.25090.11020.1372-0.0505-0.312-0.0680.0350.1487-0.1195-0.04850.45990.026-0.07590.1488-0.01090.1798-8.020433.3918-59.4183
140.6830.2857-0.12762.3439-1.02060.4474-0.02060.1549-0.42670.0273-0.1378-0.02870.1128-0.07430.08450.75080.0945-0.05190.2352-0.07770.37360.920615.9662-65.4586
150.70880.24090.1760.64910.37550.68540.11610.0765-0.175-0.3611-0.0605-0.19170.21360.1252-0.06420.42890.07170.04270.16070.00030.238615.694328.4009-53.0281
161.0667-0.7555-0.23283.39321.06850.37030.01960.1346-0.2951-0.28540.0452-0.1470.18320.1918-0.18080.70590.15620.09650.2466-0.03760.310621.859223.1422-63.0944
170.84-0.90730.39962.3648-0.47970.2135-0.06780.4258-0.1027-0.54610.0536-0.17670.04040.16290.00060.3848-0.20620.11590.7807-0.26360.4093-65.6015-20.8037-34.3851
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'D' and (resid 21 through 126 )D21 - 126
2X-RAY DIFFRACTION2chain 'D' and (resid 127 through 308 )D127 - 308
3X-RAY DIFFRACTION3chain 'D' and (resid 309 through 331 )D309 - 331
4X-RAY DIFFRACTION4chain 'A' and (resid 1 through 20 )A1 - 20
5X-RAY DIFFRACTION5chain 'A' and (resid 21 through 126 )A21 - 126
6X-RAY DIFFRACTION6chain 'A' and (resid 127 through 308 )A127 - 308
7X-RAY DIFFRACTION7chain 'A' and (resid 309 through 331 )A309 - 331
8X-RAY DIFFRACTION8chain 'B' and (resid 1 through 20 )B1 - 20
9X-RAY DIFFRACTION9chain 'B' and (resid 21 through 126 )B21 - 126
10X-RAY DIFFRACTION10chain 'B' and (resid 127 through 308 )B127 - 308
11X-RAY DIFFRACTION11chain 'B' and (resid 309 through 331 )B309 - 331
12X-RAY DIFFRACTION12chain 'C' and (resid 1 through 20 )C1 - 20
13X-RAY DIFFRACTION13chain 'C' and (resid 21 through 93 )C21 - 93
14X-RAY DIFFRACTION14chain 'C' and (resid 94 through 126 )C94 - 126
15X-RAY DIFFRACTION15chain 'C' and (resid 127 through 295 )C127 - 295
16X-RAY DIFFRACTION16chain 'C' and (resid 296 through 331 )C296 - 331
17X-RAY DIFFRACTION17chain 'D' and (resid 1 through 20 )D1 - 20

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