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Co-crystal structure of TNKS1 with compound 52 [N~2-(5-chloro-2- methoxyphenyl)-N-[trans-4-(2-oxo-2,3-dihydro-1H-benzimidazol-1-yl) CYCLOHEXYL]GLYCINAMIDE]

Analyse Co-crystal structure of TNKS1 with compound 52 [N~2-(5-chloro-2… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4K4E
Type: protein
Length: 413 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Tankyrase-1
EC: 2.4.2.30
UniProt: O95271
Ligands: K4E, ZN
Pockets: 5 · best druggability 0.72

Structure

x-ray diffraction · 2 distinct chains · 24% helix, 27% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Tankyrase-1 (EC 2.4.2.30)	protein	208	24% helix, 26% strand	O95271
B	Tankyrase-1 (EC 2.4.2.30)	protein	205	24% helix, 27% strand	O95271

Ligands and binding sites

K4E · N~2~-(5-chloro-2-methoxyphenyl)-N-[trans-4-(2-oxo-2,3-dihydro-1H-benzimidazol-1-yl)cyclohexyl]glycinamide · ligand · 2 copies · chains A, B
ZN · Zinc ion · metal · 2 copies · chains A, B

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

Pockets

5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	585	0.72	0.80	46	empty
2	452	0.67	0.79	45	K4E
3	289	0.63	0.80	32	K4E
4	55	0.38	0.80	16	empty
5	50	0.25	0.73	16	empty

Interfaces

1 interface between chains.

A–B · 260 Å² buried · 2 hydrogen bonds · protein-protein

Compared structures

4K4E · Co-crystal structure of tnks1 with compound 52… · the same entry in another collection · chain A against A, TM-score 1.00
O95271 · AlphaFold monomer V2.0 prediction for poly [ADP-ribose] polymerase tankyrase-1 (O95271) · a predicted model of the same protein · chain B against A, TM-score 0.90

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 O95271
Elsewhere: RCSB PDB 4K4E · PDBe 4K4E · UniProt O95271

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