SMTL ID : 8w23.1

Cryo-EM structure of human tankyrase 2 SAM-PARP filament bound to compound, TDI-2804 (consensus map).

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-20-mer

Ligands

20 x ZN: ZINC ION(Non-covalent)

ZN.1: 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.3: 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.5: 5 residues within 4Å: Chain C: C.644, V.646, H.647, C.652, C.655 5 PLIP interactions: 5 interactions with chain C Metal complexes: C:C.644, C:H.647, C:H.647, C:C.652, C:C.655 ZN.7: 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.9: 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.11: 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.13: 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.15: 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.17: 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.19: 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.21: 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.23: 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.25: 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.27: 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.29: 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.31: 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.33: 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.35: 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.37: 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.39: 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

20 x 01: N-{2-[4-(2-hydroxypropan-2-yl)phenyl]-4-oxo-1,4-dihydroquinazolin-7-yl}-4-methoxy-6-phenylpyridine-3-carboxamide

01.2: 16 residues within 4Å: Chain A: H.594, G.595, S.596, F.598, Y.613, M.617, F.618, Y.623, A.625, K.630, S.631, Y.634, F.673, P.692, E.701, V.703 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:F.598, A:Y.613, A:Y.613, A:F.618, A:A.625, A:K.630, A:Y.634, A:Y.634, A:P.692 Hydrogen bonds: A:G.595, A:E.701 pi-Stacking: A:F.618, A:Y.634 01.4: 15 residues within 4Å: Chain B: H.594, G.595, S.596, Y.613, M.617, F.618, Y.623, A.625, K.630, S.631, Y.634, F.673, P.692, E.701, V.703 13 PLIP interactions: 13 interactions with chain B Hydrophobic interactions: B:Y.613, B:Y.613, B:F.618, B:F.618, B:A.625, B:K.630, B:Y.634, B:Y.634, B:P.692 Hydrogen bonds: B:G.595, B:E.701 pi-Stacking: B:F.618, B:Y.634 01.6: 18 residues within 4Å: Chain C: H.594, G.595, F.598, A.612, Y.613, M.617, F.618, Y.623, A.625, K.630, S.631, Y.634, I.638, F.673, A.675, P.692, E.701, V.703 14 PLIP interactions: 14 interactions with chain C Hydrophobic interactions: C:F.598, C:Y.613, C:Y.613, C:F.618, C:F.618, C:A.625, C:K.630, C:Y.634, C:Y.634, C:I.638, C:P.692 Hydrogen bonds: C:G.595, C:E.701 pi-Stacking: C:Y.634 01.8: 19 residues within 4Å: Chain D: H.594, G.595, S.596, F.598, Y.613, M.617, F.618, Y.623, A.625, K.630, S.631, Y.634, I.638, F.673, S.674, A.675, P.692, E.701, V.703 14 PLIP interactions: 14 interactions with chain D Hydrophobic interactions: D:F.598, D:Y.613, D:Y.613, D:F.618, D:F.618, D:A.625, D:K.630, D:Y.634, D:Y.634, D:I.638, D:P.692 Hydrogen bonds: D:G.595, D:E.701 pi-Stacking: D:Y.634 01.10: 16 residues within 4Å: Chain E: H.594, G.595, S.596, F.598, Y.613, M.617, F.618, Y.623, K.630, S.631, Y.634, I.638, F.673, P.692, E.701, V.703 13 PLIP interactions: 13 interactions with chain E Hydrophobic interactions: E:F.598, E:Y.613, E:Y.613, E:F.618, E:K.630, E:Y.634, E:Y.634, E:I.638, E:P.692 Hydrogen bonds: E:G.595, E:E.701 pi-Stacking: E:F.618, E:Y.634 01.12: 18 residues within 4Å: Chain F: H.594, G.595, S.596, F.598, Y.613, M.617, F.618, Y.623, A.625, K.630, S.631, Y.634, I.638, F.673, S.674, P.692, E.701, V.703 14 PLIP interactions: 14 interactions with chain F Hydrophobic interactions: F:F.598, F:Y.613, F:Y.613, F:F.618, F:F.618, F:A.625, F:K.630, F:Y.634, F:Y.634, F:I.638, F:P.692 Hydrogen bonds: F:G.595, F:E.701 pi-Stacking: F:Y.634 01.14: 15 residues within 4Å: Chain G: H.594, G.595, S.596, F.598, Y.613, M.617, F.618, Y.623, A.625, K.630, S.631, Y.634, F.673, P.692, E.701 13 PLIP interactions: 13 interactions with chain G Hydrophobic interactions: G:F.598, G:Y.613, G:Y.613, G:F.618, G:F.618, G:A.625, G:K.630, G:Y.634, G:Y.634, G:P.692 Hydrogen bonds: G:G.595, G:E.701 pi-Stacking: G:Y.634 01.16: 17 residues within 4Å: Chain H: H.594, G.595, S.596, F.598, Y.613, M.617, F.618, Y.623, A.625, K.630, S.631, Y.634, I.638, F.673, P.692, E.701, V.703 15 PLIP interactions: 15 interactions with chain H Hydrophobic interactions: H:F.598, H:Y.613, H:Y.613, H:F.618, H:F.618, H:A.625, H:K.630, H:Y.634, H:Y.634, H:I.638, H:P.692 Hydrogen bonds: H:G.595, H:E.701 pi-Stacking: H:F.618, H:Y.634 01.18: 16 residues within 4Å: Chain I: H.594, G.595, S.596, F.598, Y.613, M.617, F.618, Y.623, A.625, K.630, S.631, Y.634, F.673, P.692, E.701, V.703 13 PLIP interactions: 13 interactions with chain I Hydrophobic interactions: I:F.598, I:Y.613, I:Y.613, I:F.618, I:F.618, I:A.625, I:K.630, I:Y.634, I:Y.634, I:P.692 Hydrogen bonds: I:G.595, I:E.701 pi-Stacking: I:Y.634 01.20: 19 residues within 4Å: Chain J: H.594, G.595, S.596, F.598, A.612, Y.613, M.617, F.618, Y.623, A.625, K.630, S.631, Y.634, I.638, F.673, R.691, P.692, E.701, V.703 16 PLIP interactions: 16 interactions with chain J Hydrophobic interactions: J:F.598, J:Y.613, J:Y.613, J:F.618, J:A.625, J:K.630, J:Y.634, J:Y.634, J:I.638, J:P.692 Hydrogen bonds: J:G.595, J:H.611, J:Y.634, J:E.701 pi-Stacking: J:F.618, J:Y.634 01.22: 20 residues within 4Å: Chain K: H.594, G.595, S.596, P.597, F.598, H.611, Y.613, M.617, F.618, Y.623, A.625, K.630, S.631, Y.634, I.638, F.673, A.675, R.691, P.692, E.701 18 PLIP interactions: 18 interactions with chain K Hydrophobic interactions: K:F.598, K:Y.613, K:Y.613, K:F.618, K:A.625, K:K.630, K:Y.634, K:Y.634, K:I.638, K:I.638, K:P.692 Hydrogen bonds: K:G.595, K:H.611, K:Y.634, K:E.701, K:E.701 pi-Stacking: K:F.618, K:Y.634 01.24: 20 residues within 4Å: Chain L: H.594, G.595, S.596, F.598, H.611, A.612, Y.613, M.617, F.618, Y.623, A.625, K.630, S.631, Y.634, I.638, F.673, R.691, P.692, E.701, V.703 15 PLIP interactions: 15 interactions with chain L Hydrophobic interactions: L:F.598, L:Y.613, L:Y.613, L:F.618, L:F.618, L:A.625, L:K.630, L:Y.634, L:Y.634, L:I.638, L:P.692 Hydrogen bonds: L:G.595, L:H.611, L:E.701 pi-Stacking: L:Y.634 01.26: 20 residues within 4Å: Chain M: H.594, G.595, S.596, F.598, Y.613, M.617, F.618, Y.623, A.625, K.630, S.631, Y.634, I.638, F.673, S.674, A.675, R.691, P.692, E.701, V.703 18 PLIP interactions: 18 interactions with chain M Hydrophobic interactions: M:F.598, M:Y.613, M:Y.613, M:F.618, M:F.618, M:A.625, M:K.630, M:Y.634, M:Y.634, M:I.638, M:I.638, M:P.692, M:E.701 Hydrogen bonds: M:G.595, M:H.611, M:Y.634, M:E.701 pi-Stacking: M:Y.634 01.28: 19 residues within 4Å: Chain N: H.594, G.595, S.596, F.598, Y.613, M.617, F.618, Y.623, K.630, S.631, Y.634, I.638, F.673, S.674, A.675, R.691, P.692, E.701, V.703 16 PLIP interactions: 16 interactions with chain N Hydrophobic interactions: N:F.598, N:Y.613, N:Y.613, N:F.618, N:F.618, N:K.630, N:Y.634, N:Y.634, N:I.638, N:I.638, N:P.692 Hydrogen bonds: N:G.595, N:H.611, N:Y.634, N:E.701 pi-Stacking: N:Y.634 01.30: 18 residues within 4Å: Chain O: H.594, G.595, S.596, F.598, Y.613, M.617, F.618, Y.623, A.625, K.630, S.631, Y.634, I.638, F.673, R.691, P.692, E.701, V.703 19 PLIP interactions: 19 interactions with chain O Hydrophobic interactions: O:F.598, O:Y.613, O:Y.613, O:F.618, O:F.618, O:A.625, O:K.630, O:Y.634, O:Y.634, O:I.638, O:I.638, O:P.692, O:E.701 Hydrogen bonds: O:G.595, O:Y.634, O:E.701, O:E.701 pi-Stacking: O:F.618, O:Y.634 01.32: 17 residues within 4Å: Chain P: H.594, G.595, S.596, F.598, Y.613, F.618, Y.623, A.625, K.630, S.631, Y.634, I.638, F.673, R.691, P.692, E.701, V.703 16 PLIP interactions: 16 interactions with chain P Hydrophobic interactions: P:F.598, P:Y.613, P:Y.613, P:F.618, P:F.618, P:A.625, P:K.630, P:Y.634, P:Y.634, P:I.638, P:I.638, P:P.692 Hydrogen bonds: P:G.595, P:Y.634, P:E.701 pi-Stacking: P:Y.634 01.34: 17 residues within 4Å: Chain Q: H.594, G.595, S.596, F.598, Y.613, M.617, F.618, Y.623, A.625, K.630, S.631, Y.634, I.638, F.673, P.692, E.701, V.703 17 PLIP interactions: 17 interactions with chain Q Hydrophobic interactions: Q:F.598, Q:Y.613, Q:Y.613, Q:F.618, Q:F.618, Q:A.625, Q:K.630, Q:Y.634, Q:Y.634, Q:I.638, Q:I.638, Q:P.692 Hydrogen bonds: Q:G.595, Q:Y.634, Q:E.701, Q:E.701 pi-Stacking: Q:Y.634 01.36: 17 residues within 4Å: Chain R: H.594, G.595, S.596, P.597, F.598, Y.613, M.617, F.618, Y.623, K.630, S.631, Y.634, I.638, F.673, P.692, E.701, V.703 16 PLIP interactions: 16 interactions with chain R Hydrophobic interactions: R:F.598, R:Y.613, R:Y.613, R:F.618, R:F.618, R:K.630, R:Y.634, R:Y.634, R:I.638, R:I.638, R:P.692 Hydrogen bonds: R:G.595, R:H.611, R:E.701, R:E.701 pi-Stacking: R:Y.634 01.38: 19 residues within 4Å: Chain S: H.594, G.595, S.596, P.597, F.598, H.611, Y.613, M.617, F.618, Y.623, A.625, K.630, S.631, Y.634, I.638, F.673, P.692, E.701, V.703 18 PLIP interactions: 18 interactions with chain S Hydrophobic interactions: S:F.598, S:Y.613, S:Y.613, S:F.618, S:F.618, S:A.625, S:K.630, S:Y.634, S:Y.634, S:I.638, S:I.638, S:P.692 Hydrogen bonds: S:G.595, S:H.611, S:Y.634, S:E.701, S:E.701 pi-Stacking: S:Y.634 01.40: 17 residues within 4Å: Chain T: H.594, G.595, S.596, Y.613, M.617, F.618, Y.623, A.625, K.630, S.631, Y.634, F.673, S.674, A.675, P.692, E.701, V.703 10 PLIP interactions: 10 interactions with chain T Hydrophobic interactions: T:Y.613, T:Y.613, T:F.618, T:A.625, T:K.630, T:Y.634, T:P.692 Hydrogen bonds: T:G.595, T:E.701 pi-Stacking: T:Y.634

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
K

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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