MolNFT v1 · #138104 · protein

Crystal structure of lactate dehydrogenase a in complex with inhibitor compound 29

5W8J · L-lactate dehydrogenase a chain: “Crystal structure of lactate dehydrogenase a in complex with inhibitor compound 29”. X-ray diffraction, 1 ligand (9Y7), 20 pockets (best druggability 0.89). MolNFT v1 #138104 on GenesisL1: 3D…

PDB: 5W8J
Type: protein
Length: 1,322 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: L-lactate dehydrogenase a chain
EC: 1.1.1.27
UniProt: P00338
Ligands: 9Y7
Pockets: 20 · best druggability 0.89

Structure

x-ray diffraction · 2 distinct chains · 45% helix, 18% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	L-lactate dehydrogenase a chain (EC 1.1.1.27)	protein	329	46% helix, 19% strand	P00338
B, C, D	L-lactate dehydrogenase a chain (EC 1.1.1.27)	protein	331	45% helix, 18% strand	P00338

Ligands and binding sites

9Y7 · 2-{3-(3,4-difluorophenyl)-5-hydroxy-4-[(4-sulfamoylphenyl)methyl]-1H-pyrazol-1-yl}-1,3-thiazole-4-carboxylic acid · ligand · 6 copies · chains A, B, C, D
MLA · Malonic acid · additive · 5 copies · chains A, C, B, D
DMS · Dimethyl sulfoxide · additive · 5 copies · chains A, C, D
GOL · Glycerol · additive · 2 copies · chains A, C, B, D

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

20 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1017	0.89	0.91	115	MLA
2	190	0.69	0.87	39	MLA
3	74	0.69	0.95	19	empty
4	66	0.66	0.94	15	empty
5	433	0.65	0.78	48	9Y7, DMS

Interfaces

6 interfaces between chains.

C–D · 2915 Å² buried · 27 hydrogen bonds · protein-protein
A–B · 2875 Å² buried · 26 hydrogen bonds · protein-protein
B–C · 1655 Å² buried · 24 hydrogen bonds · protein-protein
A–D · 1563 Å² buried · 22 hydrogen bonds · protein-protein
B–D · 957 Å² buried · 9 hydrogen bonds · protein-protein

Compared structures

5W8J · Crystal Structure of Lactate Dehydrogenase A in complex with inhibitor compound 29 · the same entry in another collection · chain A against A, TM-score 1.00

Analyse

Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
Every structure of UniProt P00338
Elsewhere: RCSB PDB 5W8J · PDBe 5W8J · UniProt P00338

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