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- PDB-6q0d: CRYSTAL STRUCTURE OF LDHA IN COMPLEX WITH COMPOUND NCGC00384414-0... -

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Basic information

Entry
Database: PDB / ID: 6q0d
TitleCRYSTAL STRUCTURE OF LDHA IN COMPLEX WITH COMPOUND NCGC00384414-01 AT 2.05 A RESOLUTION
ComponentsL-lactate dehydrogenase A chain
KeywordsOXIDOREDUCTASE/OXIDOREDUCTASE inhibitor / LDHA / OXIDOREDUCTASE-OXIDOREDUCTASE inhibitor complex
Function / homology
Function and homology information


sperm fibrous sheath / pyruvate catabolic process / L-lactate dehydrogenase / oxidoreductase complex / pyruvate metabolic process / L-lactate dehydrogenase (NAD+) activity / Pyruvate metabolism / lactate metabolic process / glucose catabolic process to lactate via pyruvate / substantia nigra development ...sperm fibrous sheath / pyruvate catabolic process / L-lactate dehydrogenase / oxidoreductase complex / pyruvate metabolic process / L-lactate dehydrogenase (NAD+) activity / Pyruvate metabolism / lactate metabolic process / glucose catabolic process to lactate via pyruvate / substantia nigra development / Regulation of pyruvate metabolism / glycolytic process / cadherin binding / mitochondrion / extracellular exosome / identical protein binding / nucleus / membrane / cytosol
Similarity search - Function
L-lactate dehydrogenase / L-lactate dehydrogenase active site. / L-lactate dehydrogenase, active site / L-2-Hydroxyisocaproate Dehydrogenase; Chain A, domain 2 / Lactate dehydrogenase/glycoside hydrolase, family 4, C-terminal / 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 ...L-lactate dehydrogenase / L-lactate dehydrogenase active site. / L-lactate dehydrogenase, active site / L-2-Hydroxyisocaproate Dehydrogenase; Chain A, domain 2 / Lactate dehydrogenase/glycoside hydrolase, family 4, C-terminal / 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 Rossmann-like Domain / NAD(P)-binding domain superfamily / Alpha-Beta Complex / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE / Chem-P8M / PHOSPHATE ION / L-lactate dehydrogenase A chain
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.05 Å
AuthorsDranow, D.M. / Davies, D.R.
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 1, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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
E: L-lactate dehydrogenase A chain
F: L-lactate dehydrogenase A chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)229,25930
Polymers220,4086
Non-polymers8,85124
Water13,583754
1
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)152,65518
Polymers146,9394
Non-polymers5,71714
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area27170 Å2
ΔGint-198 kcal/mol
Surface area41440 Å2
MethodPISA
2
E: L-lactate dehydrogenase A chain
F: L-lactate dehydrogenase A chain
hetero molecules

E: L-lactate dehydrogenase A chain
F: L-lactate dehydrogenase A chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)153,20824
Polymers146,9394
Non-polymers6,26920
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area29370 Å2
ΔGint-202 kcal/mol
Surface area41710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)212.040, 128.070, 104.140
Angle α, β, γ (deg.)90.000, 119.350, 90.000
Int Tables number5
Space group name H-MC121

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Components

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Protein , 1 types, 6 molecules ABCDEF

#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.: 6
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

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Non-polymers , 5 types, 778 molecules

#2: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: PO4
#3: Chemical
ChemComp-P8M / 2-{3-[3-(cyclopentylethynyl)-4-fluorophenyl]-5-(cyclopropylmethyl)-4-[(3-fluoro-4-sulfamoylphenyl)methyl]-1H-pyrazol-1-yl}-1,3-thiazole-4-carboxylic acid


Mass: 622.705 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C31H28F2N4O4S2 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-NAI / 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE / NADH


Mass: 665.441 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C21H29N7O14P2
#5: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 754 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.8 Å3/Da / Density % sol: 56.01 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 4.2
Details: 5% (W/V) PEG 1000, 100 MM SODIUM PHOSPHATE DIBASIC/CITRIC ACID (PH 4.2) 40% (V/V) REAGENT

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.979 Å
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: Nov 5, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.05→46.68 Å / Num. obs: 150548 / % possible obs: 99.1 % / Redundancy: 3.15 % / Biso Wilson estimate: 30.59 Å2 / Rmerge(I) obs: 0.064 / Net I/σ(I): 12.91
Reflection shellResolution: 2.05→9.7 Å / Rmerge(I) obs: 0.494 / Mean I/σ(I) obs: 2.39 / Num. unique obs: 35565 / % possible all: 99.5

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
XDSdata reduction
XSCALEdata scaling
PHASERphasing
PHENIX1.10.1_2155refinement
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5W8H

5w8h


Resolution: 2.05→46.68 Å / SU ML: 0.24 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 21.42
RfactorNum. reflection% reflection
Rfree0.225 2014 1.34 %
Rwork0.184 148527 -
obs-150541 99.3 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 118.39 Å2 / Biso mean: 38.4135 Å2 / Biso min: 14.5 Å2
Refinement stepCycle: final / Resolution: 2.05→46.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15007 0 588 754 16349
Biso mean--36 39.18 -
Num. residues----1986
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00715940
X-RAY DIFFRACTIONf_angle_d0.921738
X-RAY DIFFRACTIONf_chiral_restr0.0542543
X-RAY DIFFRACTIONf_plane_restr0.0052674
X-RAY DIFFRACTIONf_dihedral_angle_d13.8449368
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.05-2.10120.31061270.247210656100
2.1012-2.1580.261570.218310565100
2.158-2.22150.29381290.202910663100
2.2215-2.29320.25691430.200910646100
2.2932-2.37520.26441780.185110596100
2.3752-2.47030.23831660.178610642100
2.4703-2.58270.21231240.175610619100
2.5827-2.71890.21271510.171110574100
2.7189-2.88920.23621150.17471068399
2.8892-3.11220.23721440.18711056199
3.1122-3.42530.20991590.18341050799
3.4253-3.92080.22361390.17661051098
3.9208-4.93890.21751440.16761055898
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)
12.5729-1.03321.99681.6668-1.97523.7384-0.46450.08490.3179-0.19890.52240.5697-0.1653-0.3066-0.06240.30450.055-0.01360.4771-0.04230.317833.9842120.445418.2489
22.91671.7554-0.13723.2842-0.26130.5377-0.0109-0.1470.0110.23950.11390.1657-0.0030.0108-0.10020.25920.077-0.01360.2527-0.03390.225529.7325103.01341.1977
31.282-0.23640.1921.2022-0.11320.8647-0.0121-0.1591-0.26160.23880.1416-0.02250.22380.1554-0.13010.30880.0821-0.03990.265-0.02910.276639.18682.819442.5434
49.0489-8.0243-1.38799.55752.04511.69490.2853-0.272-0.3990.1858-0.18680.65130.2523-0.0805-0.08890.5926-0.01990.01860.28610.10490.44125.199575.52148.8183
52.008-2.55510.76914.2353-1.74660.8923-0.0818-0.3164-0.2450.88410.3962-0.3476-0.14680.0259-0.00010.60390.4717-0.17480.5629-0.12610.476667.062681.796146.6645
62.431.15750.50432.5046-0.2490.39690.015-0.0681-0.16150.29480.1339-0.24610.19510.2643-0.13940.32990.135-0.08160.3317-0.10620.281554.4256101.683250.6534
75.129-3.644-2.36036.50882.48393.88410.1473-0.0273-0.51580.5272-0.04910.43330.077-0.1142-0.06680.38410.0387-0.09130.2769-0.11320.288552.8727118.296461.5946
80.7844-0.05830.88420.95640.09852.2713-0.0855-0.03160.17010.0420.0901-0.1767-0.17840.1355-0.01950.26160.01060.00210.3506-0.12620.312152.1077123.915139.9302
90.84690.536-0.68710.81620.09771.49620.06520.14180.231-0.11560.07090.0445-0.204-0.0409-0.12450.31530.0328-0.01020.3277-0.08890.30146.1005122.698638.9699
102.48311.02110.67750.53820.38213.95880.057-0.01290.29060.17790.3291-0.3727-0.32450.1646-0.29220.3261-0.0003-0.07580.3601-0.16940.40761.8323130.221743.7496
112.70180.4654-0.73250.42390.67393.0884-0.11740.4185-0.2407-0.18310.1317-0.31530.30160.5560.0080.2561-0.0587-0.05530.3824-0.14030.35663.1159126.908436.4672
121.8725-0.74862.02224.3677-4.0697.2047-0.0426-0.02510.08630.02280.2581-0.1686-0.32430.5154-0.160.47560.0112-0.0460.3665-0.23150.397755.5007136.018851.3992
130.83831.5785-0.00415.2346-0.66271.5321-0.47030.29290.1122-0.14570.2727-1.0209-0.15750.63620.22540.3594-0.1116-0.07920.8125-0.1990.578170.6894123.341933.0326
141.3209-0.69660.08912.2665-0.62260.1631-0.0501-0.14250.05860.03340.1395-0.37820.09080.2569-0.08840.2770.04690.03410.5018-0.22460.416673.645597.065720.0729
151.1598-0.2778-0.27810.4785-0.33980.4445-0.08930.0729-0.26470.04350.1539-0.14510.28440.1984-0.00090.41710.166-0.05830.4425-0.2310.464663.191778.78527.3939
161.6222-0.2197-0.83130.5070.15310.7089-0.0909-0.0088-0.21920.30340.19870.04080.30720.23350.3440.36790.3318-0.00440.5443-0.3650.645777.374369.067125.1179
174.01294.6946-0.86425.7621-1.18620.3060.05960.1645-0.3333-1.01120.03291.01850.4851-0.1952-0.21140.5289-0.0667-0.06590.4251-0.15050.4835.273677.843723.8309
181.4589-1.24690.16372.8545-0.91891.2340.13580.2609-0.1518-0.37610.0036-0.00450.17020.1925-0.04940.36010.0211-0.00480.4121-0.17960.283249.337296.33926.6652
190.6348-0.39860.08541.02850.46520.948-0.04230.20270.1015-0.24470.1129-0.1781-0.0960.2375-0.05920.3094-0.05190.04040.4125-0.07830.239453.7601117.688411.8573
201.5448-0.5184-0.44941.13811.0443.2875-0.01860.20080.0012-0.84710.010.1729-0.19940.13040.01650.5138-0.046-0.02740.3863-0.01060.223146.9002123.18742.955
212.76581.3791-2.99580.7706-1.65763.58590.0457-0.1072-0.18850.0128-0.183-0.20590.02371.07010.20130.16670.00890.04320.5326-0.07040.577226.58899.4296-11.3854
220.7998-0.39240.56151.0842-0.4563.31790.04380.0783-0.1595-0.10840.0105-0.07850.28110.3007-0.00970.17230.036-0.01330.1794-0.00670.256812.344981.49336.2747
230.952-0.24520.04540.9820.19091.03880.015-0.1902-0.13610.13210.01080.09450.1007-0.1138-0.02180.2081-0.00950.01560.22080.06740.238-2.531788.960521.6408
249.0015-8.283-2.1568.38832.64352.4950.0151-0.4696-0.30930.443-0.00890.01120.17-0.08690.00120.354-0.0328-0.05860.32520.18510.33673.202978.461933.5593
251.6727-0.2812.38620.7641-0.2413.8112-0.1014-0.52730.10020.0971-0.0247-0.2066-0.61820.63320.11180.4101-0.007-0.11970.24970.00460.30149.5214104.192227.3349
263.5384-0.0823-1.61421.2539-0.19262.1350.0626-0.284-0.04330.1135-0.001-0.099-0.0580.13-0.05540.1802-0.0177-0.0220.1754-0.0040.13169.5481117.90378.301
271.95740.2045-0.00483.8471-1.64253.91540.0658-0.00510.4276-0.1280.09850.2082-0.26980.1507-0.14440.2139-0.10040.02470.2049-0.01290.256221.6031126.7657-3.1285
281.43580.38-0.02661.10030.37690.75830.01130.26630.0535-0.19090.0329-0.0614-0.11520.1465-0.03270.2148-0.04490.02380.23280.02050.196212.9156113.6369-18.2047
293.68743.69442.44598.38446.16987.1030.03930.18550.068-0.0660.1734-0.3548-0.34750.3919-0.15430.3463-0.13990.03210.40770.10290.330826.9481125.0217-20.4464
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 20 )A1 - 20
2X-RAY DIFFRACTION2chain 'A' and (resid 21 through 126 )A21 - 126
3X-RAY DIFFRACTION3chain 'A' and (resid 127 through 308 )A127 - 308
4X-RAY DIFFRACTION4chain 'A' and (resid 309 through 331 )A309 - 331
5X-RAY DIFFRACTION5chain 'B' and (resid 1 through 20 )B1 - 20
6X-RAY DIFFRACTION6chain 'B' and (resid 21 through 93 )B21 - 93
7X-RAY DIFFRACTION7chain 'B' and (resid 94 through 126 )B94 - 126
8X-RAY DIFFRACTION8chain 'B' and (resid 127 through 213 )B127 - 213
9X-RAY DIFFRACTION9chain 'B' and (resid 214 through 275 )B214 - 275
10X-RAY DIFFRACTION10chain 'B' and (resid 276 through 295 )B276 - 295
11X-RAY DIFFRACTION11chain 'B' and (resid 296 through 308 )B296 - 308
12X-RAY DIFFRACTION12chain 'B' and (resid 309 through 331 )B309 - 331
13X-RAY DIFFRACTION13chain 'C' and (resid 1 through 20 )C1 - 20
14X-RAY DIFFRACTION14chain 'C' and (resid 21 through 126 )C21 - 126
15X-RAY DIFFRACTION15chain 'C' and (resid 127 through 308 )C127 - 308
16X-RAY DIFFRACTION16chain 'C' and (resid 309 through 331 )C309 - 331
17X-RAY DIFFRACTION17chain 'D' and (resid 1 through 20 )D1 - 20
18X-RAY DIFFRACTION18chain 'D' and (resid 21 through 126 )D21 - 126
19X-RAY DIFFRACTION19chain 'D' and (resid 127 through 295 )D127 - 295
20X-RAY DIFFRACTION20chain 'D' and (resid 296 through 331 )D296 - 331
21X-RAY DIFFRACTION21chain 'E' and (resid 1 through 20 )E1 - 20
22X-RAY DIFFRACTION22chain 'E' and (resid 21 through 126 )E21 - 126
23X-RAY DIFFRACTION23chain 'E' and (resid 127 through 308 )E127 - 308
24X-RAY DIFFRACTION24chain 'E' and (resid 309 through 331 )E309 - 331
25X-RAY DIFFRACTION25chain 'F' and (resid 1 through 20 )F1 - 20
26X-RAY DIFFRACTION26chain 'F' and (resid 21 through 93 )F21 - 93
27X-RAY DIFFRACTION27chain 'F' and (resid 94 through 150 )F94 - 150
28X-RAY DIFFRACTION28chain 'F' and (resid 151 through 308 )F151 - 308
29X-RAY DIFFRACTION29chain 'F' and (resid 309 through 331 )F309 - 331

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  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

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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