5W8I: Lactate Dehydrogenase A

Crystal Structure of Lactate Dehydrogenase A in complex with inhibitor compound 23 and Zinc. Determined by X-ray diffraction at 1.95 Å resolution. Released 17 Jan 2018.

Method: X-ray diffraction
Resolution: 1.95 Å
Organism: Homo sapiens
Chains: 4
Atoms: 11,114
Mol. weight: 149.51 kDa
Ligands: MLA, CIT, 9YD, ZN
Released: 17 Jan 2018

Explore 5W8I in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5W8I contains 70 α-helices and 63 β-strands across 4 chains. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chain A: 17 helices, 15 β-strands

Element	Residues	Length	Sheet
α-helix	3-7	5
β-strand	8-10	3	1
β-strand	21-25	5	2
α-helix	29-40	12
β-strand	46-50	5	2
α-helix	54-66	13
α-helix	68-70	3
β-strand	75-78	4	2
α-helix	82-85	4
β-strand	90-93	4	2
α-helix	97-100	4
α-helix	105-126	22
α-helix	130	1
β-strand	131-134	4	2
α-helix	139-150	12
α-helix	154-156	3
β-strand	157-159	3	2
α-helix	163-177	15
α-helix	181-183	3
β-strand	184-185	2	3
β-strand	188-190	3	2
β-strand	196-198	3	2
α-helix	200-202	3
β-strand	204-205	2	3
β-strand	208-209	2	3
α-helix	210-213	4
α-helix	227-244	18
α-helix	249-263	15
β-strand	268-275	8	2
β-strand	287-295	9	2
β-strand	298-303	6	2
α-helix	309-326	18

Chain B: 18 helices, 16 β-strands

Element	Residues	Length	Sheet
α-helix	3-7	5
β-strand	8-10	3	4
β-strand	21-25	5	5
α-helix	29-40	12
β-strand	46-50	5	5
α-helix	54-66	13
α-helix	68-70	3
β-strand	75-78	4	5
α-helix	82-85	4
β-strand	90-93	4	5
α-helix	99-100	2
α-helix	105-108	4
α-helix	109-126	18
α-helix	130	1
β-strand	131-134	4	5
α-helix	139-150	12
α-helix	154-156	3
β-strand	157-159	3	5
α-helix	163-177	15
α-helix	181-183	3
β-strand	185	1	6
β-strand	188-189	2	7
β-strand	190	1	5
β-strand	197-198	2	7
α-helix	200-202	3
β-strand	204-205	2	6
β-strand	208-209	2	6
α-helix	210-213	4
α-helix	227-244	18
α-helix	249-263	15
β-strand	268-275	8	5
β-strand	287-295	9	5
β-strand	298-303	6	5
α-helix	309-326	18

Chain C: 17 helices, 16 β-strands

Element	Residues	Length	Sheet
α-helix	3-7	5
β-strand	8-10	3	5
β-strand	21-25	5	4
α-helix	29-40	12
β-strand	46-50	5	4
α-helix	54-66	13
α-helix	68-70	3
β-strand	75-78	4	4
α-helix	82-85	4
β-strand	90-93	4	4
α-helix	97-100	4
α-helix	105-126	22
α-helix	130	1
β-strand	131-134	4	4
α-helix	139-150	12
α-helix	154-156	3
β-strand	157-159	3	4
α-helix	163-177	15
α-helix	181-183	3
β-strand	185	1	8
β-strand	188-189	2	9
β-strand	190	1	4
β-strand	197-198	2	9
α-helix	200-202	3
β-strand	204-205	2	8
β-strand	208-209	2	8
α-helix	210-213	4
α-helix	227-244	18
α-helix	249-263	15
β-strand	268-275	8	4
β-strand	287-295	9	4
β-strand	298-303	6	4
α-helix	309-326	18

Chain D: 18 helices, 16 β-strands

Element	Residues	Length	Sheet
α-helix	3-7	5
β-strand	8-10	3	2
β-strand	21-25	5	1
α-helix	29-40	12
β-strand	46-50	5	1
α-helix	54-66	13
α-helix	68-70	3
β-strand	75-78	4	1
α-helix	82-85	4
β-strand	90-93	4	1
α-helix	97-100	4
α-helix	105-126	22
α-helix	130	1
β-strand	131-134	4	1
α-helix	139-150	12
α-helix	154-156	3
β-strand	157-159	3	1
α-helix	163-177	15
α-helix	181-183	3
β-strand	184-185	2	10
β-strand	188-189	2	11
β-strand	190	1	1
α-helix	193-195	3
β-strand	197-198	2	11
α-helix	200-202	3
β-strand	204-205	2	10
β-strand	208-209	2	10
α-helix	210-213	4
α-helix	227-244	18
α-helix	249-263	15
β-strand	268-275	8	1
β-strand	287-295	9	1
β-strand	298-303	6	1
α-helix	309-326	18

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
L-lactate dehydrogenase A chain	A, B, C, D	protein	332	Homo sapiens	P00338 (AlphaFold model)

Sequence of entity 1 (A, B, C, D), FASTA

>5W8I_1 L-lactate dehydrogenase A chain (chains A, B, C, D)
MATLKDQLIYNLLKEEQTPQNKITVVGVGAVGMACAISILMKDLADELALVDVIEDKLKG
EMMDLQHGSLFLRTPKIVSGKDYNVTANSKLVIITAGARQQEGESRLNLVQRNVNIFKFI
IPNVVKYSPNCKLLIVSNPVDILTYVAWKISGFPKNRVIGSGCNLDSARFRYLMGERLGV
HPLSCHGWVLGEHGDSSVPVWSGMNVAGVSLKTLHPDLGTDKDKEQWKEVHKQVVESAYE
VIKLKGYTSWAIGLSVADLAESIMKNLRRVHPVSTMIKGLYGIKDDVFLSVPCILGQNGI
SDLVKVTLTSEEEARLKKSADTLWGIQKELQF

Ligands and cofactors

ID	Name	Formula	Copies
MLA	Malonic acid	C3 H4 O4	1
CIT	Citric acid	C6 H8 O7	4
9YD	2-[3-(3,4-difluorophenyl)-5-hydroxy-1H-pyrazol-1-yl]-1,3-thiazole-4-carboxylic…	C13 H7 F2 N3 O3 S	3
ZN	Zinc ion	Zn	5

Water and common crystallization additives (DMS, GOL) are not listed.

Primary citation

Discovery and Optimization of Potent, Cell-Active Pyrazole-Based Inhibitors of Lactate Dehydrogenase (LDH). Rai, G., Brimacombe, K.R., Mott, B.T. et al. J Med Chem (2017) 60:9184-9204. DOI 10.1021/acs.jmedchem.7b00941 · PubMed

Other PDB entries of the same protein (UniProt P00338 (AlphaFold model), which also has an AlphaFold model), best resolution first:

5W8J 1.55 Å, Crystal Structure of Lactate Dehydrogenase A in complex with inhibitor compound 29
5W8K 1.6 Å, Crystal Structure of Lactate Dehydrogenase A in complex with inhibitor compound 29 and…
5W8H 1.8 Å, Crystal Structure of Lactate Dehydrogenase A in complex with inhibitor compound 11
9BK2 1.85 Å, Crystal structure of Lactate dehydrogenase in complex with…
4JNK 1.9 Å, Lactate Dehydrogenase A in complex with inhibitor compound 22
4RLS 1.91 Å, Lactate Dehydrogenase in complex with inhibitor compound 47
5W8L 1.95 Å, Crystal Structure of Lactate Dehydrogenase A in complex with inhibitor compound 59 and…
6BB0 1.95 Å, Lactate Dehydrogenase in complex with inhibitor (R)-3-((2-chlorophenyl)thio)-6-(3-((4-flu…
6MV8 1.95 Å, LDHA structure in complex with inhibitor 14
6Q13 2.0 Å, Crystal structure of ldha in complex with compound NCGC00420737-09 at 2.00 a resolution
4QO8 2.0 Å, Lactate Dehydrogenase A in complex with substituted 3-Hydroxy-2-mercaptocyclohex-2-enone…
6MVA 2.02 Å, LDHA structure in complex with inhibitor 14

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