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X-ray structure of human ldha with an allosteric inhibitor (compound 3)

Analyse X-ray structure of human ldha with an allosteric inhibitor (compound 3) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6SBU
Type: protein
Length: 2,624 residues
Chains: 8
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: L5N, NAI
Pockets: 20 · best druggability 0.83

Structure

x-ray diffraction · 1 distinct chain · 45% helix, 19% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D, E, F, G, H	L-lactate dehydrogenase a chain (EC 1.1.1.27)	protein	328	45% helix, 19% strand	P00338

Ligands and binding sites

L5N · 4-[[4-[(5-chloranylthiophen-2-yl)carbonylamino]-1,3-bis(oxidanylidene)isoindol-2-yl]methyl]benzoic acid · ligand · 8 copies · chains A, B, C, D, E, F, G, H
NAI · 1,4-dihydronicotinamide adenine dinucleotide · ligand · 2 copies · chains A, E

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

Pockets

20 pockets found on a 1 Å grid, 19 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	952	0.83	0.85	87	empty
2	678	0.81	0.85	67	empty
3	524	0.80	0.87	53	empty
4	461	0.79	0.87	49	empty
5	606	0.69	0.78	61	empty

Interfaces

14 interfaces between chains.

A–B · 2678 Å² buried · 29 hydrogen bonds · protein-protein
G–H · 2673 Å² buried · 27 hydrogen bonds · protein-protein
C–D · 2665 Å² buried · 26 hydrogen bonds · protein-protein
E–F · 2663 Å² buried · 29 hydrogen bonds · protein-protein
F–G · 1110 Å² buried · 16 hydrogen bonds · protein-protein

Compared structures

6SBU · X-ray Structure of Human LDHA with an Allosteric Inhibitor (Compound 3) · 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 6SBU · PDBe 6SBU · UniProt P00338

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