MolNFT v1 · #136892 · protein

Crystal structure of human caspase-7 soaked with allosteric inhibitor 2-{[2-(4-chlorophenyl)-2-OXOETHYL]SULFANYL}BENZOIC acid

5V6Z: “Crystal structure of human caspase-7 soaked with allosteric inhibitor…”. X-ray diffraction, 1 ligand (8YJ), 2 pockets (best druggability 0.58). MolNFT v1 #136892 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5V6Z
Type: protein
Length: 411 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: 8YJ
Pockets: 2 · best druggability 0.58

Structure

x-ray diffraction · 2 distinct chains · 34% helix, 27% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Caspase-7 (EC 3.4.22.60)	protein	201	32% helix, 27% strand	P55210
B	Caspase-7 (EC 3.4.22.60)	protein	210	35% helix, 26% strand	P55210

Ligands and binding sites

8YJ · 2-{[2-(4-chlorophenyl)-2-oxoethyl]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	362	0.58	0.75	51	8YJ
2	71	0.38	0.78	25	empty

Interfaces

1 interface between chains.

A–B · 1154 Å² buried · 16 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 1 disulfide (disulfide).

Compared structures

5V6Z · 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 5V6Z · PDBe 5V6Z · UniProt P55210

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