MolNFT v1 · #117559 · protein

Tankyrase 1 with phthalazinone 2

5EBT · Tankyrase-1: “Tankyrase 1 with phthalazinone 2”. X-ray diffraction, 2 ligands (5N8, ZN), 17 pockets (best druggability 0.78). MolNFT v1 #117559 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5EBT
Type: protein
Length: 832 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Tankyrase-1
EC: 2.4.2.30
UniProt: O95271
Ligands: 5N8, ZN
Pockets: 17 · best druggability 0.78

Structure

x-ray diffraction · 3 distinct chains · 24% helix, 28% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, C	Tankyrase-1 (EC 2.4.2.30)	protein	210	24% helix, 28% strand	O95271
B	Tankyrase-1 (EC 2.4.2.30)	protein	206	24% helix, 29% strand	O95271
D	Tankyrase-1 (EC 2.4.2.30)	protein	206	24% helix, 28% strand	O95271

Ligands and binding sites

5N8 · 4-[bis(fluoranyl)-[3-[[(6~{S})-6-methyl-3-(trifluoromethyl)-6,8-dihydro-5~{H}-[1,2,4]triazolo[4,3-a]pyrazin-7-yl]carbonyl]phenyl]methyl]-2~{H}-phthalazin-1-one · ligand · 4 copies · chains A, B, C, D
ZN · Zinc ion · metal · 4 copies · chains A, B, C, D
BU3 · (R,R)-2,3-butanediol · additive · 2 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, 11 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	909	0.78	0.81	83	empty
2	1004	0.72	0.76	78	empty
3	382	0.72	0.83	33	5N8
4	576	0.71	0.79	58	empty
5	496	0.71	0.80	39	empty

Interfaces

5 interfaces between chains.

A–D · 921 Å² buried · 10 hydrogen bonds · protein-protein
B–C · 736 Å² buried · 12 hydrogen bonds · protein-protein
A–B · 549 Å² buried · 6 hydrogen bonds · protein-protein
C–D · 349 Å² buried · 0 hydrogen bonds · protein-protein
B–D · 100 Å² buried · 1 hydrogen bond · protein-protein

Compared structures

5EBT · Tankyrase 1 with Phthalazi 2 · 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 O95271
Elsewhere: RCSB PDB 5EBT · PDBe 5EBT · UniProt O95271

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