8HKS

Mutated human ADP-ribosyltransferase 2 (PARP2) catalytic domain bound to Pamiparib(BGB-290)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.238 
  • R-Value Work: 0.181 
  • R-Value Observed: 0.184 

Starting Model: in silico
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.0 of the entry. See complete history


Literature

Mutated human ADP-ribosyltransferase 2 (PARP2) catalytic domain bound to Pamiparib

Wang, X.Y.Zhou, J.Xu, B.L.

To be published.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Poly [ADP-ribose] polymerase 2
A, B, C, D
353Homo sapiensMutation(s): 4 
Gene Names: PARP2ADPRT2ADPRTL2
EC: 2.4.2.30 (PDB Primary Data), 2.4.2 (PDB Primary Data)
UniProt & NIH Common Fund Data Resources
Find proteins for Q9UGN5 (Homo sapiens)
Explore Q9UGN5 
Go to UniProtKB:  Q9UGN5
PHAROS:  Q9UGN5
GTEx:  ENSG00000129484 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9UGN5
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
DS9 (Subject of Investigation/LOI)
Query on DS9

Download Ideal Coordinates CCD File 
G [auth A],
M [auth B],
P [auth C],
T [auth D]
(2R)-14-fluoro-2-methyl-6,9,10,19-tetrazapentacyclo[14.2.1.02,6.08,18.012,17]nonadeca-1(18),8,12(17),13,15-pentaen-11-one
C16 H15 F N4 O
DENYZIUJOTUUNY-MRXNPFEDSA-N
GOL
Query on GOL

Download Ideal Coordinates CCD File 
E [auth A]
F [auth A]
H [auth B]
I [auth B]
J [auth B]
E [auth A],
F [auth A],
H [auth B],
I [auth B],
J [auth B],
K [auth B],
L [auth B],
N [auth C],
O [auth C],
Q [auth D],
R [auth D],
S [auth D]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
DS9 BindingDB:  8HKS IC50: min: 0.11, max: 500 (nM) from 4 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.238 
  • R-Value Work: 0.181 
  • R-Value Observed: 0.184 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 81.006α = 90
b = 86.333β = 112.44
c = 103.619γ = 90
Software Package:
Software NamePurpose
autoPROCdata processing
MOLREPphasing
Aimlessdata scaling
PHENIXrefinement

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China82003657
National Natural Science Foundation of China (NSFC)China81673300
National Natural Science Foundation of China (NSFC)China82173693

Revision History  (Full details and data files)

  • Version 1.0: 2024-05-01
    Type: Initial release