MolNFT v1 · #16030 · protein

Extendend tethering: in situ assembly of inhibitors

1NMQ · Caspase-3: “Extendend tethering: in situ assembly of inhibitors”. X-ray diffraction, 1 ligand (160), 4 pockets (best druggability 0.65). MolNFT v1 #16030 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 1NMQ
Type: protein
Length: 476 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Caspase-3
EC: 3.4.22.-
UniProt: P42574
Ligands: 160
Pockets: 4 · best druggability 0.65

Structure

x-ray diffraction · 1 distinct chain · 28% helix, 26% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Caspase-3 (EC 3.4.22.-)	protein	238	28% helix, 26% strand	P42574

Ligands and binding sites

160 · 3-(3-{2-[(5-methanesulfonyl-thiophene-2-carbonyl)-amino]-ethyldisulfanylmethyl}- benzenesulfonylamino)-4-oxo-pentanoic acid · ligand · 2 copies · chains A, B

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

Pockets

4 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	311	0.65	0.80	35	empty
2	217	0.48	0.75	39	160
3	222	0.48	0.74	32	160
4	67	0.33	0.75	15	empty

Interfaces

1 interface between chains.

A–B · 2413 Å² buried · 41 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 1 covalent (covalent ligand).

Compared structures

1NMQ · Extendend Tethering: In Situ Assembly of Inhibitors · the same entry in another collection · chain A against A, 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 0.97

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 1NMQ · PDBe 1NMQ · UniProt P42574

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