5Y65

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 
  • R-Value Work: 0.198 
  • R-Value Observed: 0.200 

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Ligand Structure Quality Assessment 


This is version 1.0 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
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(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
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  • 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 
  • R-Value Work: 0.198 
  • R-Value Observed: 0.200 
  • 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

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Ligand Structure Quality Assessment 


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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