MolNFT v1 · #178823 · protein

Crystal structure of schistosome BCL-2 bound to abt-737

7JMT · BCL-2 protein: “Crystal structure of schistosome BCL-2 bound to abt-737”. X-ray diffraction, 1 ligand (N3C), 13 pockets (best druggability 0.67). MolNFT v1 #178823 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 7JMT
Type: protein
Length: 955 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: BCL-2 protein
UniProt: Q5BWX6
Ligands: N3C
Pockets: 13 · best druggability 0.67

Structure

x-ray diffraction · 5 distinct chains · 72% helix, 0% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, F	BCL-2 protein	protein	161	73% helix, 0% strand	Q5BWX6
B	BCL-2 protein	protein	156	69% helix, 0% strand	Q5BWX6
C	BCL-2 protein	protein	165	73% helix, 0% strand	Q5BWX6
D	BCL-2 protein	protein	156	71% helix, 0% strand	Q5BWX6
E	BCL-2 protein	protein	156	73% helix, 0% strand	Q5BWX6

Ligands and binding sites

N3C · 4-{4-[(4'-chlorobiphenyl-2-yl)methyl]piperazin-1-yl}-N-{[4-({(1R)-3-(dimethylamino)-1-[(phenylthio) methyl]propyl}amino)-3-nitrophenyl]sulfonyl}benzamide · ligand · 6 copies · chains A, B, C, D, E, F

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

Pockets

13 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	381	0.67	0.80	31	N3C
2	389	0.60	0.75	54	empty
3	124	0.59	0.85	32	empty
4	196	0.57	0.80	29	empty
5	281	0.56	0.76	36	empty

Interfaces

6 interfaces between chains.

B–C · 605 Å² buried · 13 hydrogen bonds · protein-protein
A–F · 572 Å² buried · 11 hydrogen bonds · protein-protein
D–E · 538 Å² buried · 10 hydrogen bonds · protein-protein
C–D · 456 Å² buried · 1 hydrogen bond · protein-protein
E–F · 355 Å² buried · 1 hydrogen bond · protein-protein

Compared structures

7JMT · Crystal structure of schistosome BCL-2 bound to ABT-737 · 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 Q5BWX6
Elsewhere: RCSB PDB 7JMT · PDBe 7JMT · UniProt Q5BWX6

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