MolNFT v1 · #103541 · protein

Structure of PARP1 catalytic domain bound to inhibitor bmn 673

4PJT · Poly [ADP-ribose] polymerase 1: “Structure of PARP1 catalytic domain bound to inhibitor bmn 673”. X-ray diffraction, 2 ligands (2YQ, SO4), 17 pockets (best druggability 0.78). MolNFT v1 #103541 on GenesisL1: 3D structure, binding…

PDB: 4PJT
Type: protein
Length: 1,342 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Poly [ADP-ribose] polymerase 1
EC: 2.4.2.30
UniProt: P09874
Ligands: 2YQ, SO4
Pockets: 17 · best druggability 0.78

Structure

x-ray diffraction · 4 distinct chains · 39% helix, 25% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Poly [ADP-ribose] polymerase 1 (EC 2.4.2.30)	protein	338	39% helix, 25% strand	P09874
B	Poly [ADP-ribose] polymerase 1 (EC 2.4.2.30)	protein	332	40% helix, 25% strand	P09874
C	Poly [ADP-ribose] polymerase 1 (EC 2.4.2.30)	protein	346	39% helix, 25% strand	P09874
D	Poly [ADP-ribose] polymerase 1 (EC 2.4.2.30)	protein	326	39% helix, 25% strand	P09874

Ligands and binding sites

2YQ · (8S,9R)-5-fluoro-8-(4-fluorophenyl)-9-(1-methyl-1H-1,2, 4-triazol-5-yl)-2,7,8,9-tetrahydro-3H-pyrido[4,3,2-de]phthalazin-3-one · ligand · 4 copies · chains A, B, C, D
SO4 · Sulfate ion · ion · 15 copies · chains A, B, C, D
GOL · Glycerol · additive · 3 copies · chains A, C

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	515	0.78	0.85	44	SO4, 2YQ
2	532	0.78	0.85	43	2YQ, GOL
3	495	0.77	0.84	45	SO4, 2YQ
4	558	0.77	0.83	45	2YQ
5	875	0.73	0.77	81	SO4

Interfaces

5 interfaces between chains.

A–C · 647 Å² buried · 8 hydrogen bonds · protein-protein
A–B · 441 Å² buried · 5 hydrogen bonds · protein-protein
C–D · 348 Å² buried · 3 hydrogen bonds · protein-protein
B–C · 346 Å² buried · 0 hydrogen bonds · protein-protein
B–D · 186 Å² buried · 0 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 2 disulfide (disulfide).

Compared structures

4PJT · Structure of PARP1 catalytic domain bound to inhibitor BMN 673 · 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 P09874
Elsewhere: RCSB PDB 4PJT · PDBe 4PJT · UniProt P09874

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