SMTL ID : 6mck.1

p97 D1D2 with CB5083 bound

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.77 Å

Oligo State

homo-12-mer

Ligands

12 x JDP: 1-[4-(benzylamino)-7,8-dihydro-5H-pyrano[4,3-d]pyrimidin-2-yl]-2-methyl-1H-indole-4-carboxamide(Non-covalent)

JDP.1: 15 residues within 4Å: Chain A: V.266, D.270, I.271, L.274, C.314, G.315, L.318, A.447, I.448, A.451, N.452, R.454, G.476, A.477, T.480 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:I.271, A:I.271, A:L.274, A:I.448, A:A.451 Hydrogen bonds: A:A.447, A:R.454, A:T.480 JDP.2: 15 residues within 4Å: Chain B: V.266, D.270, I.271, L.274, C.314, G.315, L.318, A.447, I.448, A.451, N.452, R.454, G.476, A.477, T.480 8 PLIP interactions: 8 interactions with chain B Hydrophobic interactions: B:I.271, B:I.271, B:L.274, B:I.448, B:A.451 Hydrogen bonds: B:D.270, B:A.447, B:R.454 JDP.3: 15 residues within 4Å: Chain C: V.266, D.270, I.271, L.274, C.314, G.315, L.318, S.444, A.447, I.448, A.451, R.454, G.476, A.477, T.480 8 PLIP interactions: 8 interactions with chain C Hydrophobic interactions: C:I.271, C:I.271, C:L.274, C:I.448, C:A.451 Hydrogen bonds: C:D.270, C:A.447, C:R.454 JDP.4: 17 residues within 4Å: Chain D: V.266, D.270, I.271, L.274, C.314, G.315, L.318, L.319, S.444, A.447, I.448, A.451, N.452, R.454, G.476, A.477, T.480 8 PLIP interactions: 8 interactions with chain D Hydrophobic interactions: D:I.271, D:I.271, D:L.274, D:L.319, D:I.448, D:I.448 Hydrogen bonds: D:A.447, D:R.454 JDP.5: 17 residues within 4Å: Chain E: V.266, D.270, I.271, L.274, C.314, G.315, L.318, L.319, S.444, A.447, I.448, A.451, N.452, R.454, G.476, A.477, T.480 11 PLIP interactions: 11 interactions with chain E Hydrophobic interactions: E:I.271, E:I.271, E:L.274, E:L.318, E:L.319, E:I.448, E:I.448, E:A.451 Hydrogen bonds: E:A.447, E:R.454, E:T.480 JDP.6: 16 residues within 4Å: Chain F: V.266, D.270, I.271, L.274, C.314, G.315, L.318, L.319, S.444, A.447, I.448, A.451, R.454, G.476, A.477, T.480 6 PLIP interactions: 6 interactions with chain F Hydrophobic interactions: F:I.271, F:I.271, F:L.274, F:L.319 Hydrogen bonds: F:R.454, F:T.480 JDP.7: 15 residues within 4Å: Chain G: V.266, D.270, I.271, L.274, C.314, G.315, L.318, S.444, I.448, A.451, N.452, R.454, G.476, A.477, T.480 8 PLIP interactions: 8 interactions with chain G Hydrophobic interactions: G:I.271, G:I.271, G:L.274, G:I.448, G:I.448, G:A.451 Hydrogen bonds: G:A.447, G:R.454 JDP.8: 16 residues within 4Å: Chain H: V.266, D.270, I.271, L.274, C.314, G.315, L.318, L.319, A.447, I.448, A.451, N.452, R.454, G.476, A.477, T.480 10 PLIP interactions: 10 interactions with chain H Hydrophobic interactions: H:I.271, H:I.271, H:L.274, H:L.319, H:I.448, H:I.448, H:I.448 Hydrogen bonds: H:D.270, H:A.447, H:R.454 JDP.9: 16 residues within 4Å: Chain I: V.266, D.270, I.271, L.274, C.314, G.315, L.318, L.319, S.444, I.448, A.451, N.452, R.454, G.476, A.477, T.480 9 PLIP interactions: 9 interactions with chain I Hydrophobic interactions: I:I.271, I:I.271, I:L.274, I:L.319, I:I.448, I:A.451 Hydrogen bonds: I:D.270, I:A.447, I:R.454 JDP.10: 17 residues within 4Å: Chain J: V.266, D.270, I.271, L.274, C.314, G.315, L.318, L.319, S.444, A.447, I.448, A.451, N.452, R.454, G.476, A.477, T.480 9 PLIP interactions: 9 interactions with chain J Hydrophobic interactions: J:I.271, J:I.271, J:L.274, J:L.319, J:I.448, J:A.451 Hydrogen bonds: J:A.447, J:R.454, J:T.480 JDP.11: 17 residues within 4Å: Chain K: V.266, D.270, I.271, L.274, C.314, G.315, L.318, L.319, S.444, A.447, I.448, A.451, N.452, R.454, G.476, A.477, T.480 9 PLIP interactions: 9 interactions with chain K Hydrophobic interactions: K:I.271, K:I.271, K:L.274, K:L.319, K:I.448, K:I.448 Hydrogen bonds: K:A.447, K:R.454, K:T.480 JDP.12: 16 residues within 4Å: Chain L: V.266, D.270, I.271, L.274, C.314, G.315, L.318, S.444, A.447, I.448, A.451, N.452, R.454, G.476, A.477, T.480 8 PLIP interactions: 8 interactions with chain L Hydrophobic interactions: L:I.271, L:I.271, L:L.274, L:I.448, L:A.451 Hydrogen bonds: L:A.447, L:R.454, L:T.480

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Tang, W.K. et al., Structural Basis of p97 Inhibition by the Site-Selective Anticancer Compound CB-5083. Mol. Pharmacol. (2019)

Release Date

2019-01-23

Peptides

Transitional endoplasmic reticulum ATPase: ABCDEFGHIJKL

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
K

L
L

Transitional endoplasmic reticulum ATPase