6MCK | pdb_00006mck

p97 D1D2 with CB5083 bound


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.77 Å
  • R-Value Free: 
    0.265 (Depositor), 0.260 (DCC) 
  • R-Value Work: 
    0.222 (Depositor), 0.227 (DCC) 
  • R-Value Observed: 
    0.224 (Depositor) 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.4 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

  • DOI: https://doi.org/10.1124/mol.118.114256
  • Primary Citation of Related Structures:  
    6MCK

  • PubMed Abstract: 

    Inhibition of p97, a key player in the ubiquitin-proteasome degradation pathway, has been proposed as a treatment of cancer. This concept was nearly realized recently when a potent p97 inhibitor, 1-[4-(benzylamino)-5H,7H,8H-pyrano[4,3-d]pyrimidin-2-yl]-2-methyl-1H-indole-4-carboxamide (CB-5083), was developed and demonstrated broad antitumor activity in various tumor models. CB-5083 functions as a competitive inhibitor that binds selectively to the ATP-binding site of the D2 domain, although both the D1 and D2 ATPase sites of p97 are highly similar. Despite its promising anticancer activity, CB-5083 failed its phase I clinical trials due to an unexpected off-target effect, which necessitates further improvement of the inhibitor. In this study, we determined the crystal structure of N-terminal domain-truncated p97 in complex with CB-5083. It provides a structural basis for the specificity of CB-5083 toward the D2 domain, offers an explanation in atomic detail for the mutations that confer resistance to CB-5083, and establishes a foundation for future structure-guided efforts to develop the next generation of p97 inhibitors.


  • Organizational Affiliation

    Laboratory of Cell Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Transitional endoplasmic reticulum ATPase
A, B, C, D, E
A, B, C, D, E, F, G, H, I, J, K, L
606Homo sapiensMutation(s): 0 
Gene Names: VCP
EC: 3.6.4.6
UniProt & NIH Common Fund Data Resources
Find proteins for P55072 (Homo sapiens)
Explore P55072 
Go to UniProtKB:  P55072
PHAROS:  P55072
GTEx:  ENSG00000165280 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP55072
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
JDP
Query on JDP

Download Ideal Coordinates CCD File 
M [auth A]
N [auth B]
O [auth C]
P [auth D]
Q [auth E]
M [auth A],
N [auth B],
O [auth C],
P [auth D],
Q [auth E],
R [auth F],
S [auth G],
T [auth H],
U [auth I],
V [auth J],
W [auth K],
X [auth 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
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.77 Å
  • R-Value Free:  0.265 (Depositor), 0.260 (DCC) 
  • R-Value Work:  0.222 (Depositor), 0.227 (DCC) 
  • R-Value Observed: 0.224 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 127.41α = 90
b = 263.83β = 103.67
c = 164.13γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2019-01-23
    Type: Initial release
  • Version 1.1: 2019-01-30
    Changes: Data collection, Database references
  • Version 1.2: 2019-02-13
    Changes: Data collection, Database references
  • Version 1.3: 2024-03-13
    Changes: Data collection, Database references, Refinement description
  • Version 1.4: 2025-06-11
    Changes: Structure summary