MolNFT v1 · #136888 · protein

Crystal structure of human caspase-7 soaked with allosteric inhibitor 2-[(2-ACETYLPHENYL)SULFANYL]BENZOIC acid

5V6U: “Crystal structure of human caspase-7 soaked with allosteric inhibitor 2-[(2-ACETYLPHENYL)SULFANYL]BENZOIC acid”. X-ray diffraction, 1 ligand (8YM), 2 pockets (best druggability 0.66). MolNFT v1 #136888 on GenesisL1: 3D structure…

PDB: 5V6U
Type: protein
Length: 418 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Caspase-7
EC: 3.4.22.60
UniProt: P55210
Ligands: 8YM
Pockets: 2 · best druggability 0.66

Structure

x-ray diffraction · 2 distinct chains · 32% helix, 27% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Caspase-7 (EC 3.4.22.60)	protein	205	32% helix, 28% strand	P55210
B	Caspase-7 (EC 3.4.22.60)	protein	213	33% helix, 26% strand	P55210

Ligands and binding sites

8YM · 2-[(2-acetylphenyl)sulfanyl]benzoic acid · ligand · chains B

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	621	0.66	0.76	45	8YM
2	50	0.33	0.78	14	empty

Interfaces

1 interface between chains.

A–B · 1407 Å² buried · 20 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 2 disulfide (disulfide).

Compared structures

5V6U · Crystal structure of human caspase-7 soaked with allosteric inhibitor… · the same entry in another collection · chain A against A, TM-score 1.00
P55210 · AlphaFold monomer V2.0 prediction for caspase-7 (P55210) · a predicted model of the same protein · chain A against A, TM-score 0.99

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 P55210
Elsewhere: RCSB PDB 5V6U · PDBe 5V6U · UniProt P55210

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