4XJS

Human CD38 complexed with inhibitor 1 [6-fluoro-2-methyl-4-[(2,3,6-trichlorobenzyl)amino]quinoline-8-carboxamide]

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.263 
  • R-Value Work: 0.186 
  • R-Value Observed: 0.190 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 2.1 of the entry. See complete history. 



Macromolecules
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(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase 1262Homo sapiensMutation(s): 4 
Gene Names: CD38
EC: 3.2.2.6 (PDB Primary Data), 2.4.99.20 (PDB Primary Data)
UniProt & NIH Common Fund Data Resources
Find proteins for P28907 (Homo sapiens)
Explore P28907 
Go to UniProtKB:  P28907
PHAROS:  P28907
GTEx:  ENSG00000004468 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP28907
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
733
Query on 733
Download Ideal Coordinates CCD File 
B [auth A]6-fluoro-2-methyl-4-[(2,3,6-trichlorobenzyl)amino]quinoline-8-carboxamide
C18 H13 Cl3 F N3 O
CFRVEJULVHOSOC-UHFFFAOYSA-N
HSX
Query on HSX
Download Ideal Coordinates CCD File 
C [auth A]5-O-phosphono-alpha-D-ribofuranose
C5 H11 O8 P
KTVPXOYAKDPRHY-AIHAYLRMSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
733 BindingDB:  4XJS IC50: 76 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.263 
  • R-Value Work: 0.186 
  • R-Value Observed: 0.190 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 50.298α = 90
b = 64.424β = 90
c = 72.832γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-2000data reduction
SCALEPACKdata scaling
REFMACphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


View more in-depth experimental data
Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2015-08-26
    Type: Initial release
  • Version 1.1: 2015-09-09
    Changes: Database references
  • Version 1.2: 2015-09-23
    Changes: Database references
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Data collection, Database references, Derived calculations
  • Version 2.1: 2023-09-27
    Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary