MolNFT v1 · #181699 · protein

Crystal structure of human lactate dehydrogenase a with inhibitor compound 15

7M2N · L-lactate dehydrogenase a chain: “Crystal structure of human lactate dehydrogenase a with inhibitor compound 15”. X-ray diffraction, 3 ligands (NAI, YOJ, SO4), 18 pockets (best druggability 0.89). MolNFT v1 #181699 on GenesisL1: 3D…

PDB: 7M2N
Type: protein
Length: 1,320 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: NAI, YOJ, SO4
Pockets: 18 · best druggability 0.89

Structure

x-ray diffraction · 3 distinct chains · 45% helix, 20% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	L-lactate dehydrogenase a chain (EC 1.1.1.27)	protein	327	46% helix, 19% strand	P00338
B	L-lactate dehydrogenase a chain (EC 1.1.1.27)	protein	331	45% helix, 21% strand	P00338
C, D	L-lactate dehydrogenase a chain (EC 1.1.1.27)	protein	331	45% helix, 19% strand	P00338

Ligands and binding sites

NAI · 1,4-dihydronicotinamide adenine dinucleotide · ligand · 4 copies · chains A, B, C, D
YOJ · 5-[(5'-{1-(4-carboxy-1,3-thiazol-2-yl)-5-(cyclopropylmethyl)-4-[(3-fluoro-4-sulfamoylphenyl) methyl]-1H-pyrazol-3-yl}-2'-fluoro[1,1'-biphenyl]-4-yl)oxy]-1H-1,2,3-triazole-4-carboxylic acid · ligand · 4 copies · chains A, B, C, D
SO4 · Sulfate ion · ion · 10 copies · chains A, C, B, D
EDO · 1,2-ethanediol · additive · 75 copies · chains A, B, C, D
GOL · Glycerol · additive · 6 copies · chains A, B, C, D
PEG · Di(hydroxyethyl)ether · additive · 6 copies · chains A, D, B, C

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

Pockets

18 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1067	0.89	0.91	115	SO4, EDO, PEG, GOL
2	848	0.73	0.78	78	EDO, NAI, PEG, YOJ
3	846	0.73	0.77	74	NAI, YOJ, EDO
4	80	0.72	0.95	19	empty
5	81	0.70	0.94	17	empty

Interfaces

6 interfaces between chains.

A–B · 2906 Å² buried · 26 hydrogen bonds · protein-protein
C–D · 2900 Å² buried · 30 hydrogen bonds · protein-protein
A–D · 1723 Å² buried · 27 hydrogen bonds · protein-protein
B–C · 1670 Å² buried · 30 hydrogen bonds · protein-protein
B–D · 992 Å² buried · 9 hydrogen bonds · protein-protein

Compared structures

7M2N · Crystal structure of Human Lactate Dehydrogenase A with Inhibitor Compound 15 · 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 7M2N · PDBe 7M2N · UniProt P00338

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