6MCK

p97 D1D2 with CB5083 bound


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.77 Å
  • R-Value Free: 0.265 
  • R-Value Work: 0.222 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structural Basis of p97 Inhibition by the Site-Selective Anticancer Compound CB-5083.

Tang, W.K.Odzorig, T.Jin, W.Xia, D.

(2019) Mol. Pharmacol. 95: 286-293


Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Transitional endoplasmic reticulum ATPase
A, B, C, D, E, F, G, H, I, J, K, L
606Homo sapiensMutation(s): 0 
Gene Names: VCP
EC: 3.6.4.6
Find proteins for P55072 (Homo sapiens)
Go to Gene View: VCP
Go to UniProtKB:  P55072
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
JDP
Query on JDP

Download SDF File 
Download CCD File 
A, B, C, D, E, F, G, H, I, J, K, L
1-[4-(benzylamino)-7,8-dihydro-5H-pyrano[4,3-d]pyrimidin-2-yl]-2-methyl-1H-indole-4-carboxamide
C24 H23 N5 O2
RDALZZCKQFLGJP-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.77 Å
  • R-Value Free: 0.265 
  • R-Value Work: 0.222 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 127.410α = 90.00
b = 263.830β = 103.67
c = 164.130γ = 90.00
Software Package:
Software NamePurpose
MOLREPphasing
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2018-08-31 
  • Released Date: 2019-01-23 
  • Deposition Author(s): Xia, D., Tang, W.K.

Revision History 

  • Version 1.0: 2019-01-23
    Type: Initial release
  • Version 1.1: 2019-01-30
    Type: Data collection, Database references
  • Version 1.2: 2019-02-13
    Type: Data collection, Database references