SMTL ID : 6kro.1

Tankyrase-2 in complex with RK-582

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

hetero-1-1-mer

Ligands

1 x DU9: 6-[(2S,6R)-2,6-dimethylmorpholin-4-yl]-4-fluoranyl-1-methyl-1'-(8-methyl-4-oxidanylidene-3,5,6,7-tetrahydropyrido[2,3-d]pyrimidin-2-yl)spiro[indole-3,4'-piperidine]-2-one(Non-covalent)

DU9.1: 20 residues within 4Å: Chain A: F.84, H.85, G.86, S.87, P.88, F.89, H.102, A.103, Y.104, Y.114, F.115, A.116, K.121, S.122, Y.125, G.128, I.129 Chain B: E.24 Ligands: GOL.4, GOL.5 12 PLIP interactions: 1 interactions with chain B, 11 interactions with chain A Hydrophobic interactions: B:E.24, A:P.88, A:Y.104, A:A.116, A:K.121, A:Y.125, A:I.129, A:I.129 Hydrogen bonds: A:G.86, A:G.86 pi-Stacking: A:F.89, A:Y.125

1 x ZN: ZINC ION(Non-covalent)

ZN.2: 4 residues within 4Å: Chain A: C.135, H.138, C.143, C.146 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.135, A:H.138, A:C.143, A:C.146

1 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.3: 6 residues within 4Å: Chain A: R.31, H.33, R.34, D.35, K.121, Q.124 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:R.34, A:D.35, A:Q.124 Water bridges: A:R.31, A:R.34 Salt bridges: A:R.31, A:H.33, A:R.34, A:K.121

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 7 residues within 4Å: Chain A: H.85, S.87, I.93, D.99, H.102, A.103 Ligands: DU9.1 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.87, A:S.87, A:D.99, A:D.99 GOL.5: 8 residues within 4Å: Chain A: Y.104, G.107, M.108, F.109, K.121, Y.125 Chain B: E.24 Ligands: DU9.1 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:M.108, A:K.121, A:Y.125

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Shirai, F. et al., Design and Discovery of an Orally Efficacious Spiroindolinone-Based Tankyrase Inhibitor for the Treatment of Colon Cancer. J.Med.Chem. (2020)

Release Date

2020-04-01

Peptides

Tankyrase-2: A
Tankyrase-2: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Tankyrase-2

Tankyrase-2

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