SMTL ID : 8w27.1

Cryo-EM structure of human tankyrase 2 SAM-PARP filament bound to compound, XAV (consensus map).

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-20-mer

Ligands

20 x XAV: 2-[4-(trifluoromethyl)phenyl]-7,8-dihydro-5H-thiopyrano[4,3-d]pyrimidin-4-ol(Non-covalent)

XAV.1: 13 residues within 4Å: Chain A: H.594, G.595, S.596, F.598, Y.613, Y.623, F.624, A.625, K.630, S.631, Y.634, I.638, E.701 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:Y.613, A:Y.613, A:Y.634, A:Y.634, A:I.638 Hydrogen bonds: A:H.594, A:G.595, A:G.595 pi-Stacking: A:Y.634 XAV.3: 14 residues within 4Å: Chain B: H.594, G.595, S.596, P.597, F.598, Y.613, Y.623, F.624, A.625, K.630, S.631, Y.634, I.638, E.701 10 PLIP interactions: 10 interactions with chain B Hydrophobic interactions: B:Y.613, B:Y.613, B:Y.623, B:Y.634, B:Y.634, B:I.638 Hydrogen bonds: B:H.594, B:G.595, B:G.595 pi-Stacking: B:Y.634 XAV.5: 13 residues within 4Å: Chain C: H.594, G.595, S.596, F.598, Y.613, Y.623, F.624, A.625, K.630, S.631, Y.634, I.638, E.701 8 PLIP interactions: 8 interactions with chain C Hydrophobic interactions: C:Y.613, C:Y.613, C:Y.634, C:Y.634, C:I.638 Hydrogen bonds: C:G.595, C:G.595 pi-Stacking: C:Y.634 XAV.7: 14 residues within 4Å: Chain D: H.594, G.595, S.596, P.597, F.598, Y.613, Y.623, F.624, A.625, K.630, S.631, Y.634, I.638, E.701 8 PLIP interactions: 8 interactions with chain D Hydrophobic interactions: D:Y.613, D:Y.613, D:Y.634, D:Y.634, D:I.638 Hydrogen bonds: D:G.595, D:G.595 pi-Stacking: D:Y.634 XAV.9: 14 residues within 4Å: Chain E: H.594, G.595, S.596, P.597, F.598, Y.613, Y.623, F.624, A.625, K.630, S.631, Y.634, I.638, E.701 11 PLIP interactions: 11 interactions with chain E Hydrophobic interactions: E:Y.613, E:Y.613, E:Y.623, E:Y.634, E:Y.634, E:I.638 Hydrogen bonds: E:H.594, E:G.595, E:G.595 pi-Stacking: E:Y.634 Halogen bonds: E:S.596 XAV.11: 14 residues within 4Å: Chain F: H.594, G.595, S.596, P.597, F.598, Y.613, Y.623, F.624, A.625, K.630, S.631, Y.634, I.638, E.701 8 PLIP interactions: 8 interactions with chain F Hydrophobic interactions: F:Y.613, F:Y.613, F:Y.634, F:Y.634 Hydrogen bonds: F:H.594, F:G.595, F:G.595 pi-Stacking: F:Y.634 XAV.13: 14 residues within 4Å: Chain G: H.594, G.595, S.596, P.597, F.598, Y.613, Y.623, F.624, A.625, K.630, S.631, Y.634, I.638, E.701 8 PLIP interactions: 8 interactions with chain G Hydrophobic interactions: G:Y.613, G:Y.613, G:Y.634, G:Y.634, G:I.638 Hydrogen bonds: G:G.595, G:G.595 pi-Stacking: G:Y.634 XAV.15: 14 residues within 4Å: Chain H: H.594, G.595, S.596, P.597, F.598, Y.613, Y.623, F.624, A.625, K.630, S.631, Y.634, I.638, E.701 9 PLIP interactions: 9 interactions with chain H Hydrophobic interactions: H:Y.613, H:Y.613, H:Y.623, H:Y.634, H:Y.634, H:I.638 Hydrogen bonds: H:G.595, H:G.595 pi-Stacking: H:Y.634 XAV.17: 14 residues within 4Å: Chain I: H.594, G.595, S.596, P.597, F.598, Y.613, Y.623, F.624, A.625, K.630, S.631, Y.634, I.638, E.701 9 PLIP interactions: 9 interactions with chain I Hydrophobic interactions: I:Y.613, I:Y.613, I:Y.623, I:Y.634, I:Y.634, I:I.638 Hydrogen bonds: I:G.595, I:G.595 pi-Stacking: I:Y.634 XAV.19: 12 residues within 4Å: Chain J: H.594, G.595, S.596, F.598, Y.613, Y.623, F.624, A.625, K.630, S.631, Y.634, E.701 6 PLIP interactions: 6 interactions with chain J Hydrophobic interactions: J:Y.613, J:Y.613, J:Y.634 Hydrogen bonds: J:G.595, J:G.595 pi-Stacking: J:Y.634 XAV.21: 13 residues within 4Å: Chain K: H.594, G.595, S.596, F.598, Y.613, Y.623, F.624, A.625, K.630, S.631, Y.634, I.638, E.701 9 PLIP interactions: 9 interactions with chain K Hydrophobic interactions: K:Y.613, K:Y.613, K:Y.623, K:Y.634, K:Y.634, K:I.638 Hydrogen bonds: K:G.595, K:G.595 pi-Stacking: K:Y.634 XAV.23: 13 residues within 4Å: Chain L: H.594, G.595, S.596, F.598, Y.613, Y.623, F.624, A.625, K.630, S.631, Y.634, I.638, E.701 8 PLIP interactions: 8 interactions with chain L Hydrophobic interactions: L:Y.613, L:Y.613, L:Y.634, L:Y.634, L:I.638 Hydrogen bonds: L:G.595, L:G.595 pi-Stacking: L:Y.634 XAV.25: 13 residues within 4Å: Chain M: H.594, G.595, S.596, F.598, Y.613, Y.623, F.624, A.625, K.630, S.631, Y.634, I.638, E.701 8 PLIP interactions: 8 interactions with chain M Hydrophobic interactions: M:Y.613, M:Y.613, M:Y.634, M:Y.634, M:I.638 Hydrogen bonds: M:G.595, M:G.595 pi-Stacking: M:Y.634 XAV.27: 13 residues within 4Å: Chain N: H.594, G.595, S.596, F.598, Y.613, Y.623, F.624, A.625, K.630, S.631, Y.634, I.638, E.701 8 PLIP interactions: 8 interactions with chain N Hydrophobic interactions: N:Y.613, N:Y.613, N:Y.634, N:Y.634, N:I.638 Hydrogen bonds: N:G.595, N:G.595 pi-Stacking: N:Y.634 XAV.29: 14 residues within 4Å: Chain O: H.594, G.595, S.596, P.597, F.598, Y.613, Y.623, F.624, A.625, K.630, S.631, Y.634, I.638, E.701 9 PLIP interactions: 9 interactions with chain O Hydrophobic interactions: O:Y.613, O:Y.613, O:Y.623, O:Y.634, O:Y.634, O:I.638 Hydrogen bonds: O:G.595, O:G.595 pi-Stacking: O:Y.634 XAV.31: 13 residues within 4Å: Chain P: H.594, G.595, S.596, F.598, Y.613, Y.623, F.624, A.625, K.630, S.631, Y.634, I.638, E.701 8 PLIP interactions: 8 interactions with chain P Hydrophobic interactions: P:Y.613, P:Y.613, P:Y.634, P:Y.634, P:I.638 Hydrogen bonds: P:G.595, P:G.595 pi-Stacking: P:Y.634 XAV.33: 14 residues within 4Å: Chain Q: H.594, G.595, S.596, P.597, F.598, Y.613, Y.623, F.624, A.625, K.630, S.631, Y.634, I.638, E.701 8 PLIP interactions: 8 interactions with chain Q Hydrophobic interactions: Q:Y.613, Q:Y.613, Q:Y.634, Q:Y.634, Q:I.638 Hydrogen bonds: Q:G.595, Q:G.595 pi-Stacking: Q:Y.634 XAV.35: 14 residues within 4Å: Chain R: H.594, G.595, S.596, P.597, F.598, Y.613, Y.623, F.624, A.625, K.630, S.631, Y.634, I.638, E.701 9 PLIP interactions: 9 interactions with chain R Hydrophobic interactions: R:Y.613, R:Y.613, R:Y.623, R:Y.634, R:Y.634, R:I.638 Hydrogen bonds: R:G.595, R:G.595 pi-Stacking: R:Y.634 XAV.37: 13 residues within 4Å: Chain S: H.594, G.595, S.596, F.598, Y.613, Y.623, F.624, A.625, K.630, S.631, Y.634, I.638, E.701 8 PLIP interactions: 8 interactions with chain S Hydrophobic interactions: S:Y.613, S:Y.613, S:Y.634, S:Y.634, S:I.638 Hydrogen bonds: S:G.595, S:G.595 pi-Stacking: S:Y.634 XAV.39: 12 residues within 4Å: Chain T: H.594, G.595, S.596, F.598, Y.613, Y.623, F.624, A.625, K.630, S.631, Y.634, E.701 7 PLIP interactions: 7 interactions with chain T Hydrophobic interactions: T:Y.613, T:Y.613, T:Y.634, T:Y.634 Hydrogen bonds: T:G.595, T:G.595 pi-Stacking: T:Y.634

20 x ZN: ZINC ION(Non-covalent)

ZN.2: 4 residues within 4Å: Chain A: C.644, H.647, C.652, C.655 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.644, A:H.647, A:C.652, A:C.655 ZN.4: 4 residues within 4Å: Chain B: C.644, H.647, C.652, C.655 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:C.644, B:H.647, B:C.652, B:C.655 ZN.6: 4 residues within 4Å: Chain C: C.644, H.647, C.652, C.655 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:C.644, C:H.647, C:C.652, C:C.655 ZN.8: 4 residues within 4Å: Chain D: C.644, H.647, C.652, C.655 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:C.644, D:H.647, D:C.652, D:C.655 ZN.10: 4 residues within 4Å: Chain E: C.644, H.647, C.652, C.655 4 PLIP interactions: 4 interactions with chain E Metal complexes: E:C.644, E:H.647, E:C.652, E:C.655 ZN.12: 4 residues within 4Å: Chain F: C.644, H.647, C.652, C.655 4 PLIP interactions: 4 interactions with chain F Metal complexes: F:C.644, F:H.647, F:C.652, F:C.655 ZN.14: 4 residues within 4Å: Chain G: C.644, H.647, C.652, C.655 4 PLIP interactions: 4 interactions with chain G Metal complexes: G:C.644, G:H.647, G:C.652, G:C.655 ZN.16: 4 residues within 4Å: Chain H: C.644, H.647, C.652, C.655 4 PLIP interactions: 4 interactions with chain H Metal complexes: H:C.644, H:H.647, H:C.652, H:C.655 ZN.18: 4 residues within 4Å: Chain I: C.644, H.647, C.652, C.655 4 PLIP interactions: 4 interactions with chain I Metal complexes: I:C.644, I:H.647, I:C.652, I:C.655 ZN.20: 4 residues within 4Å: Chain J: C.644, H.647, C.652, C.655 4 PLIP interactions: 4 interactions with chain J Metal complexes: J:C.644, J:H.647, J:C.652, J:C.655 ZN.22: 4 residues within 4Å: Chain K: C.644, H.647, C.652, C.655 4 PLIP interactions: 4 interactions with chain K Metal complexes: K:C.644, K:H.647, K:C.652, K:C.655 ZN.24: 4 residues within 4Å: Chain L: C.644, H.647, C.652, C.655 4 PLIP interactions: 4 interactions with chain L Metal complexes: L:C.644, L:H.647, L:C.652, L:C.655 ZN.26: 4 residues within 4Å: Chain M: C.644, H.647, C.652, C.655 4 PLIP interactions: 4 interactions with chain M Metal complexes: M:C.644, M:H.647, M:C.652, M:C.655 ZN.28: 4 residues within 4Å: Chain N: C.644, H.647, C.652, C.655 4 PLIP interactions: 4 interactions with chain N Metal complexes: N:C.644, N:H.647, N:C.652, N:C.655 ZN.30: 4 residues within 4Å: Chain O: C.644, H.647, C.652, C.655 4 PLIP interactions: 4 interactions with chain O Metal complexes: O:C.644, O:H.647, O:C.652, O:C.655 ZN.32: 4 residues within 4Å: Chain P: C.644, H.647, C.652, C.655 4 PLIP interactions: 4 interactions with chain P Metal complexes: P:C.644, P:H.647, P:C.652, P:C.655 ZN.34: 4 residues within 4Å: Chain Q: C.644, H.647, C.652, C.655 4 PLIP interactions: 4 interactions with chain Q Metal complexes: Q:C.644, Q:H.647, Q:C.652, Q:C.655 ZN.36: 4 residues within 4Å: Chain R: C.644, H.647, C.652, C.655 4 PLIP interactions: 4 interactions with chain R Metal complexes: R:C.644, R:H.647, R:C.652, R:C.655 ZN.38: 4 residues within 4Å: Chain S: C.644, H.647, C.652, C.655 4 PLIP interactions: 4 interactions with chain S Metal complexes: S:C.644, S:H.647, S:C.652, S:C.655 ZN.40: 4 residues within 4Å: Chain T: C.644, H.647, C.652, C.655 4 PLIP interactions: 4 interactions with chain T Metal complexes: T:C.644, T:H.647, T:C.652, T:C.655

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zimmerman, J. et al., A potent and selective TNKS2 inhibitor for tumor-selective WNT suppression. Biorxiv (2025)

Release Date

2025-07-09

Peptides

Maltose/maltodextrin-binding periplasmic protein,Poly [ADP-ribose] polymerase tankyrase-2: ABCDEFGHIJKLMNOPQRST

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

G
G

H
H

I
I

J
J

K
L

L
M

M
N

N
O

O
P

P
Q

Q
R

R
S

S
T

T
U

Maltose/maltodextrin-binding periplasmic protein,Poly [ADP-ribose] polymerase tankyrase-2

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