MolNFT v1 · #186723 · protein

Crystal structure of caspase-3 with inhibitor ac-ykpvd-cho

7RNE · Caspase-3 subunit P17: “Crystal structure of caspase-3 with inhibitor ac-ykpvd-cho”. X-ray diffraction, 2 pockets (best druggability 0.65). MolNFT v1 #186723 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 7RNE
Type: protein
Length: 471 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Caspase-3 subunit P17; Caspase-3 subunit P12; Ac-ykpvd-cho
UniProt: P42574
Pockets: 2 · best druggability 0.65

Structure

x-ray diffraction · 4 distinct chains · 28% helix, 30% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Caspase-3 subunit P17	protein	141	25% helix, 30% strand	P42574
B, D	Caspase-3 subunit P12	protein	92	34% helix, 22% strand	P42574
C	Caspase-3 subunit P17	protein	140	27% helix, 34% strand	P42574
F, G	Ac-ykpvd-cho	protein	3	0% helix, 33% strand	—

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	297	0.65	0.80	36	empty
2	67	0.31	0.75	17	empty

Interfaces

10 interfaces between chains.

A–B · 2150 Å² buried · 32 hydrogen bonds · protein-protein
C–D · 2118 Å² buried · 29 hydrogen bonds · protein-protein
B–D · 1507 Å² buried · 24 hydrogen bonds · protein-protein
A–D · 432 Å² buried · 8 hydrogen bonds · protein-protein
B–C · 411 Å² buried · 9 hydrogen bonds · protein-protein

Compared structures

7RNE · Crystal structure of caspase-3 with inhibitor Ac-YKPVD-CHO · the same entry in another collection · chain B against B, TM-score 1.00
P42574 · AlphaFold monomer V2.0 prediction for caspase-3 (P42574) · 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 P42574
Elsewhere: RCSB PDB 7RNE · PDBe 7RNE · UniProt P42574

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