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

ID or keywords:

Entry

Database: PDB / ID: 6q0d

Title

CRYSTAL STRUCTURE OF LDHA IN COMPLEX WITH COMPOUND NCGC00384414-01 AT 2.05 A RESOLUTION

Components

L-lactate dehydrogenase A chain

Keywords

OXIDOREDUCTASE/OXIDOREDUCTASE inhibitor /

LDHA / OXIDOREDUCTASE-OXIDOREDUCTASE inhibitor complex

Function / homology

Function and homology information

oxidoreductase complex / lactate metabolic process /

Pyruvate metabolism /

L-lactate dehydrogenase /

L-lactate dehydrogenase activity / pyruvate metabolic process / substantia nigra development / glycolytic process /

cadherin binding /

mitochondrion ...
Similarity search - Function

Biological species

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT /

molecular replacement / Resolution: 2.05 Å

Authors

Dranow, D.M. / Davies, D.R.

Citation

Journal: 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. / ...

History

Deposition	Aug 1, 2019	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Sep 23, 2020	Provider: repository / Type: Initial release
Revision 1.1	Oct 7, 2020	Group: Database references / Category: citation / citation_author Item: _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2	Oct 21, 2020	Group: 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 1.3	Oct 11, 2023	Group: 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

Structure viewer	Molecule: MolmilJmol/JSmol

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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/q0/6q0d ftp://data.pdbj.org/pub/pdb/validation_reports/q0/6q0d	HTTPS FTP

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Related structure data

Related structure data	6q13C 5w8hS S: Starting model for refinement C: citing same article (ref.)
Similar structure data	5w8l-2 4zvv-d 5ixy-d 4qo8-d 4r68-d 3pqd-1 5w8j-d 3d0o-1 5w8l-1 5nqq-d Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#102 - Jun 2008 Lactate Dehydrogenase similarity (11) #154 - Oct 2012 Citric Acid Cycle similarity (6) #142 - Oct 2011 PDB Pioneers similarity (10) #93 - Sep 2007 Citrate Synthase similarity (1)

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

229 kDa, 6 polymers
Search similar-shape structures of this assembly by Omokage search (details)

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

defined by author&software
153 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

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

defined by author&software
153 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

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 number	5
Space group name H-M	C121

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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

#1: Protein

L-lactate dehydrogenase A chain / LDH-A / Cell proliferation-inducing gene 19 protein / LDH muscle subunit / LDH-M / Renal carcinoma ...

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 / Phosphate 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 / Nicotinamide adenine dinucleotide 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 / Glycerol Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C₃H₈O₃
#6: Water	ChemComp-HOH / water / 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 interest	Y

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal	Density Matthews: 2.8 Å³/Da / Density % sol: 56.01 %
Crystal grow	Temperature: 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

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

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Phasing

Phasing	Method: molecular replacement

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Processing

Software

Name	Version	Classification
XDS		data reduction
XSCALE		data scaling
PHASER		phasing
PHENIX	1.10.1_2155	refinement
PDB_EXTRACT	3.25	data extraction

Refinement

Method 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

	R_factor	Num. reflection	% reflection
R_free	0.225	2014	1.34 %
R_work	0.184	148527	-
obs	-	150541	99.3 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL

Displacement parameters

B_iso max: 118.39 Å² / B_iso mean: 38.4135 Å² / B_iso min: 14.5 Å²

Refinement step

Cycle: final / Resolution: 2.05→46.68 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	15007	0	588	754	16349
B_iso mean	-	-	36	39.18	-
Num. residues	-	-	-	-	1986

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.007	15940
X-RAY DIFFRACTION	f_angle_d	0.9	21738
X-RAY DIFFRACTION	f_chiral_restr	0.054	2543
X-RAY DIFFRACTION	f_plane_restr	0.005	2674
X-RAY DIFFRACTION	f_dihedral_angle_d	13.844	9368

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / R_factor R_free error: 0

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	% reflection obs (%)
2.05-2.1012	0.3106	127	0.2472	10656	100
2.1012-2.158	0.26	157	0.2183	10565	100
2.158-2.2215	0.2938	129	0.2029	10663	100
2.2215-2.2932	0.2569	143	0.2009	10646	100
2.2932-2.3752	0.2644	178	0.1851	10596	100
2.3752-2.4703	0.2383	166	0.1786	10642	100
2.4703-2.5827	0.2123	124	0.1756	10619	100
2.5827-2.7189	0.2127	151	0.1711	10574	100
2.7189-2.8892	0.2362	115	0.1747	10683	99
2.8892-3.1122	0.2372	144	0.1871	10561	99
3.1122-3.4253	0.2099	159	0.1834	10507	99
3.4253-3.9208	0.2236	139	0.1766	10510	98
3.9208-4.9389	0.2175	144	0.1676	10558	98

Refinement TLS params.

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

ID	L11 (°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)
1	2.5729	-1.0332	1.9968	1.6668	-1.9752	3.7384	-0.4645	0.0849	0.3179	-0.1989	0.5224	0.5697	-0.1653	-0.3066	-0.0624	0.3045	0.055	-0.0136	0.4771	-0.0423	0.3178	33.9842	120.4454	18.2489
2	2.9167	1.7554	-0.1372	3.2842	-0.2613	0.5377	-0.0109	-0.147	0.011	0.2395	0.1139	0.1657	-0.003	0.0108	-0.1002	0.2592	0.077	-0.0136	0.2527	-0.0339	0.2255	29.7325	103.013	41.1977
3	1.282	-0.2364	0.192	1.2022	-0.1132	0.8647	-0.0121	-0.1591	-0.2616	0.2388	0.1416	-0.0225	0.2238	0.1554	-0.1301	0.3088	0.0821	-0.0399	0.265	-0.0291	0.2766	39.186	82.8194	42.5434
4	9.0489	-8.0243	-1.3879	9.5575	2.0451	1.6949	0.2853	-0.272	-0.399	0.1858	-0.1868	0.6513	0.2523	-0.0805	-0.0889	0.5926	-0.0199	0.0186	0.2861	0.1049	0.441	25.1995	75.521	48.8183
5	2.008	-2.5551	0.7691	4.2353	-1.7466	0.8923	-0.0818	-0.3164	-0.245	0.8841	0.3962	-0.3476	-0.1468	0.0259	-0.0001	0.6039	0.4717	-0.1748	0.5629	-0.1261	0.4766	67.0626	81.7961	46.6645
6	2.43	1.1575	0.5043	2.5046	-0.249	0.3969	0.015	-0.0681	-0.1615	0.2948	0.1339	-0.2461	0.1951	0.2643	-0.1394	0.3299	0.135	-0.0816	0.3317	-0.1062	0.2815	54.4256	101.6832	50.6534
7	5.129	-3.644	-2.3603	6.5088	2.4839	3.8841	0.1473	-0.0273	-0.5158	0.5272	-0.0491	0.4333	0.077	-0.1142	-0.0668	0.3841	0.0387	-0.0913	0.2769	-0.1132	0.2885	52.8727	118.2964	61.5946
8	0.7844	-0.0583	0.8842	0.9564	0.0985	2.2713	-0.0855	-0.0316	0.1701	0.042	0.0901	-0.1767	-0.1784	0.1355	-0.0195	0.2616	0.0106	0.0021	0.3506	-0.1262	0.3121	52.1077	123.9151	39.9302
9	0.8469	0.536	-0.6871	0.8162	0.0977	1.4962	0.0652	0.1418	0.231	-0.1156	0.0709	0.0445	-0.204	-0.0409	-0.1245	0.3153	0.0328	-0.0102	0.3277	-0.0889	0.301	46.1005	122.6986	38.9699
10	2.4831	1.0211	0.6775	0.5382	0.3821	3.9588	0.057	-0.0129	0.2906	0.1779	0.3291	-0.3727	-0.3245	0.1646	-0.2922	0.3261	-0.0003	-0.0758	0.3601	-0.1694	0.407	61.8323	130.2217	43.7496
11	2.7018	0.4654	-0.7325	0.4239	0.6739	3.0884	-0.1174	0.4185	-0.2407	-0.1831	0.1317	-0.3153	0.3016	0.556	0.008	0.2561	-0.0587	-0.0553	0.3824	-0.1403	0.356	63.1159	126.9084	36.4672
12	1.8725	-0.7486	2.0222	4.3677	-4.069	7.2047	-0.0426	-0.0251	0.0863	0.0228	0.2581	-0.1686	-0.3243	0.5154	-0.16	0.4756	0.0112	-0.046	0.3665	-0.2315	0.3977	55.5007	136.0188	51.3992
13	0.8383	1.5785	-0.0041	5.2346	-0.6627	1.5321	-0.4703	0.2929	0.1122	-0.1457	0.2727	-1.0209	-0.1575	0.6362	0.2254	0.3594	-0.1116	-0.0792	0.8125	-0.199	0.5781	70.6894	123.3419	33.0326
14	1.3209	-0.6966	0.0891	2.2665	-0.6226	0.1631	-0.0501	-0.1425	0.0586	0.0334	0.1395	-0.3782	0.0908	0.2569	-0.0884	0.277	0.0469	0.0341	0.5018	-0.2246	0.4166	73.6455	97.0657	20.0729
15	1.1598	-0.2778	-0.2781	0.4785	-0.3398	0.4445	-0.0893	0.0729	-0.2647	0.0435	0.1539	-0.1451	0.2844	0.1984	-0.0009	0.4171	0.166	-0.0583	0.4425	-0.231	0.4646	63.1917	78.785	27.3939
16	1.6222	-0.2197	-0.8313	0.507	0.1531	0.7089	-0.0909	-0.0088	-0.2192	0.3034	0.1987	0.0408	0.3072	0.2335	0.344	0.3679	0.3318	-0.0044	0.5443	-0.365	0.6457	77.3743	69.0671	25.1179
17	4.0129	4.6946	-0.8642	5.7621	-1.1862	0.306	0.0596	0.1645	-0.3333	-1.0112	0.0329	1.0185	0.4851	-0.1952	-0.2114	0.5289	-0.0667	-0.0659	0.4251	-0.1505	0.48	35.2736	77.8437	23.8309
18	1.4589	-1.2469	0.1637	2.8545	-0.9189	1.234	0.1358	0.2609	-0.1518	-0.3761	0.0036	-0.0045	0.1702	0.1925	-0.0494	0.3601	0.0211	-0.0048	0.4121	-0.1796	0.2832	49.3372	96.3392	6.6652
19	0.6348	-0.3986	0.0854	1.0285	0.4652	0.948	-0.0423	0.2027	0.1015	-0.2447	0.1129	-0.1781	-0.096	0.2375	-0.0592	0.3094	-0.0519	0.0404	0.4125	-0.0783	0.2394	53.7601	117.6884	11.8573
20	1.5448	-0.5184	-0.4494	1.1381	1.044	3.2875	-0.0186	0.2008	0.0012	-0.8471	0.01	0.1729	-0.1994	0.1304	0.0165	0.5138	-0.046	-0.0274	0.3863	-0.0106	0.2231	46.9002	123.1874	2.955
21	2.7658	1.3791	-2.9958	0.7706	-1.6576	3.5859	0.0457	-0.1072	-0.1885	0.0128	-0.183	-0.2059	0.0237	1.0701	0.2013	0.1667	0.0089	0.0432	0.5326	-0.0704	0.5772	26.588	99.4296	-11.3854
22	0.7998	-0.3924	0.5615	1.0842	-0.456	3.3179	0.0438	0.0783	-0.1595	-0.1084	0.0105	-0.0785	0.2811	0.3007	-0.0097	0.1723	0.036	-0.0133	0.1794	-0.0067	0.2568	12.3449	81.4933	6.2747
23	0.952	-0.2452	0.0454	0.982	0.1909	1.0388	0.015	-0.1902	-0.1361	0.1321	0.0108	0.0945	0.1007	-0.1138	-0.0218	0.2081	-0.0095	0.0156	0.2208	0.0674	0.238	-2.5317	88.9605	21.6408
24	9.0015	-8.283	-2.156	8.3883	2.6435	2.495	0.0151	-0.4696	-0.3093	0.443	-0.0089	0.0112	0.17	-0.0869	0.0012	0.354	-0.0328	-0.0586	0.3252	0.1851	0.3367	3.2029	78.4619	33.5593
25	1.6727	-0.281	2.3862	0.7641	-0.241	3.8112	-0.1014	-0.5273	0.1002	0.0971	-0.0247	-0.2066	-0.6182	0.6332	0.1118	0.4101	-0.007	-0.1197	0.2497	0.0046	0.3014	9.5214	104.1922	27.3349
26	3.5384	-0.0823	-1.6142	1.2539	-0.1926	2.135	0.0626	-0.284	-0.0433	0.1135	-0.001	-0.099	-0.058	0.13	-0.0554	0.1802	-0.0177	-0.022	0.1754	-0.004	0.1316	9.5481	117.9037	8.301
27	1.9574	0.2045	-0.0048	3.8471	-1.6425	3.9154	0.0658	-0.0051	0.4276	-0.128	0.0985	0.2082	-0.2698	0.1507	-0.1444	0.2139	-0.1004	0.0247	0.2049	-0.0129	0.2562	21.6031	126.7657	-3.1285
28	1.4358	0.38	-0.0266	1.1003	0.3769	0.7583	0.0113	0.2663	0.0535	-0.1909	0.0329	-0.0614	-0.1152	0.1465	-0.0327	0.2148	-0.0449	0.0238	0.2328	0.0205	0.1962	12.9156	113.6369	-18.2047
29	3.6874	3.6944	2.4459	8.3844	6.1698	7.103	0.0393	0.1855	0.068	-0.066	0.1734	-0.3548	-0.3475	0.3919	-0.1543	0.3463	-0.1399	0.0321	0.4077	0.1029	0.3308	26.9481	125.0217	-20.4464

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 1 through 20 )	A	1 - 20
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 21 through 126 )	A	21 - 126
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 127 through 308 )	A	127 - 308
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 309 through 331 )	A	309 - 331
5	X-RAY DIFFRACTION	5	chain 'B' and (resid 1 through 20 )	B	1 - 20
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 21 through 93 )	B	21 - 93
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 94 through 126 )	B	94 - 126
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 127 through 213 )	B	127 - 213
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 214 through 275 )	B	214 - 275
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 276 through 295 )	B	276 - 295
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 296 through 308 )	B	296 - 308
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 309 through 331 )	B	309 - 331
13	X-RAY DIFFRACTION	13	chain 'C' and (resid 1 through 20 )	C	1 - 20
14	X-RAY DIFFRACTION	14	chain 'C' and (resid 21 through 126 )	C	21 - 126
15	X-RAY DIFFRACTION	15	chain 'C' and (resid 127 through 308 )	C	127 - 308
16	X-RAY DIFFRACTION	16	chain 'C' and (resid 309 through 331 )	C	309 - 331
17	X-RAY DIFFRACTION	17	chain 'D' and (resid 1 through 20 )	D	1 - 20
18	X-RAY DIFFRACTION	18	chain 'D' and (resid 21 through 126 )	D	21 - 126
19	X-RAY DIFFRACTION	19	chain 'D' and (resid 127 through 295 )	D	127 - 295
20	X-RAY DIFFRACTION	20	chain 'D' and (resid 296 through 331 )	D	296 - 331
21	X-RAY DIFFRACTION	21	chain 'E' and (resid 1 through 20 )	E	1 - 20
22	X-RAY DIFFRACTION	22	chain 'E' and (resid 21 through 126 )	E	21 - 126
23	X-RAY DIFFRACTION	23	chain 'E' and (resid 127 through 308 )	E	127 - 308
24	X-RAY DIFFRACTION	24	chain 'E' and (resid 309 through 331 )	E	309 - 331
25	X-RAY DIFFRACTION	25	chain 'F' and (resid 1 through 20 )	F	1 - 20
26	X-RAY DIFFRACTION	26	chain 'F' and (resid 21 through 93 )	F	21 - 93
27	X-RAY DIFFRACTION	27	chain 'F' and (resid 94 through 150 )	F	94 - 150
28	X-RAY DIFFRACTION	28	chain 'F' and (resid 151 through 308 )	F	151 - 308
29	X-RAY DIFFRACTION	29	chain 'F' and (resid 309 through 331 )	F	309 - 331

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