5Y65 | pdb_00005y65

Phosphoglycerate mutase 1 complexed with a small molecule inhibitor KH2

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.55 Å
  • R-Value Free: 
    0.248 (Depositor), 0.250 (DCC) 
  • R-Value Work: 
    0.198 (Depositor), 0.200 (DCC) 
  • R-Value Observed: 
    0.200 (Depositor) 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted HKBClick on this verticalbar to view details

This is version 1.1 of the entry. See complete history. 


Literature

Phosphoglycerate mutase 1 complexed with a small molecule inhibitor KH2

Jiang, L.L., Zhou, L.

To be published.

Macromolecules
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(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Phosphoglycerate mutase 1A [auth B]262Homo sapiensMutation(s): 0 
Gene Names: PGAM1, PGAMA, CDABP0006
EC: 5.4.2.11 (PDB Primary Data), 5.4.2.4 (PDB Primary Data)
UniProt & NIH Common Fund Data Resources
Find proteins for P18669 (Homo sapiens)
Explore P18669 
Go to UniProtKB:  P18669
PHAROS:  P18669
GTEx:  ENSG00000171314 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP18669
Sequence Annotations
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  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Phosphoglycerate mutase 1B [auth C]262Homo sapiensMutation(s): 0 
Gene Names: PGAM1, PGAMA, CDABP0006
EC: 5.4.2.11 (PDB Primary Data), 5.4.2.4 (PDB Primary Data)
UniProt & NIH Common Fund Data Resources
Find proteins for P18669 (Homo sapiens)
Explore P18669 
Go to UniProtKB:  P18669
PHAROS:  P18669
GTEx:  ENSG00000171314 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP18669
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
HKB
Query on HKB
Download Ideal Coordinates CCD File 
E [auth C]~{N}-[3,4-bis(oxidanyl)-9,10-bis(oxidanylidene)anthracen-2-yl]-4-(dimethylamino)benzenesulfonamide
C22 H18 N2 O6 S
CJPMCWRDXYBEBQ-UHFFFAOYSA-N
MES
Query on MES
Download Ideal Coordinates CCD File 
D [auth C]2-(N-MORPHOLINO)-ETHANESULFONIC ACID
C6 H13 N O4 S
SXGZJKUKBWWHRA-UHFFFAOYSA-N
CL
Query on CL
Download Ideal Coordinates CCD File 
C [auth B]CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
NEP
Query on NEP		B [auth C]L-PEPTIDE LINKINGC6 H10 N3 O5 PHIS
Binding Affinity Annotations 
IDSourceBinding Affinity
HKB BindingDB:  5Y65 IC50: 770 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.55 Å
  • R-Value Free:  0.248 (Depositor), 0.250 (DCC) 
  • R-Value Work:  0.198 (Depositor), 0.200 (DCC) 
  • R-Value Observed: 0.200 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 79.193α = 90
b = 82.929β = 90
c = 99.797γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
HKL-2000data scaling
PHASERphasing
PHENIXrefinement
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted HKBClick on this verticalbar to view details

View more in-depth experimental data
Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
National Science Foundation (China)China21472026

Revision History  (Full details and data files)

  • Version 1.0: 2018-12-05
    Type: Initial release
  • Version 1.1: 2025-04-09
    Changes: Data collection, Database references, Structure summary