MolNFT v1 · #166607 · protein

Crystal structure of BCL-xl bound to compound 15: (R)-2-(3-(2-((4'- chloro-[1,1'-biphenyl]-2-YL)METHYL)-1,2,3,4-tetrahydroisoquinoline-6- carbonyl)-3-(4-METHYLBENZYL)UREIDO)-3-((CYCLOHEXYLMETHYL)SULFONYL) propanoic acid

6UVH · BCL-2-like protein 1: “Crystal structure of BCL-xl bound to compound 15: (R)-2-(3-(2-((4'…”. X-ray diffraction, 2 ligands (QHJ, SO4), 10 pockets (best druggability 0.61). MolNFT v1 #166607 on GenesisL1: 3D structure, binding sites…

PDB: 6UVH
Type: protein
Length: 561 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: BCL-2-like protein 1
UniProt: Q07817
Ligands: QHJ, SO4
Pockets: 10 · best druggability 0.61

Structure

x-ray diffraction · 2 distinct chains · 80% helix, 0% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	BCL-2-like protein 1	protein	141	81% helix, 0% strand	Q07817
B, C, D	BCL-2-like protein 1	protein	140	79% helix, 0% strand	Q07817

Ligands and binding sites

QHJ · (R)-2-(3-(2-((4'-chloro-[1,1'-biphenyl]-2-yl)methyl)-1, 2,3,4-tetrahydroisoquinoline-6-carbonyl)-3-(4-methylbenzyl)ureido)-3-((cyclohexylmethyl)sulfonyl) propanoic acid · ligand · 4 copies · chains A, B, C, D
SO4 · Sulfate ion · ion · 2 copies · chains A, C, D
EDO · 1,2-ethanediol · additive · chains A

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

Pockets

10 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	312	0.61	0.78	38	EDO, SO4, QHJ
2	288	0.59	0.79	41	empty
3	224	0.58	0.80	37	empty
4	62	0.51	0.86	15	empty
5	80	0.42	0.79	15	empty

Interfaces

4 interfaces between chains.

C–D · 2216 Å² buried · 31 hydrogen bonds · protein-protein
A–B · 2188 Å² buried · 30 hydrogen bonds · protein-protein
A–C · 731 Å² buried · 9 hydrogen bonds · protein-protein
B–C · 181 Å² buried · 3 hydrogen bonds · protein-protein

Compared structures

6UVH · Crystal structure of BCL-XL bound to compound 15… · the same entry in another collection · chain D against D, TM-score 1.00
Q07817 · AlphaFold monomer V2.0 prediction for BCL-2-like protein 1 (Q07817) · a predicted model of the same protein · chain B against A, TM-score 0.80

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 Q07817
Elsewhere: RCSB PDB 6UVH · PDBe 6UVH · UniProt Q07817

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