5SD8

Crystal Structure of Dihydrofolate Reductase from Homo sapiens bound to NADP and SDDC Inhibitor SDDC-1190 (racemic mixture)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.05 Å
  • R-Value Free: 0.180 
  • R-Value Work: 0.162 
  • R-Value Observed: 0.163 

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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Crystal Structure of Dihydrofolate Reductase from Homo sapiens bound to NADP and SDDC Inhibitor SDDC-1190 (racemic mixture)

Mayclin, S.J.Fairman, J.W.Dranow, D.M.Conrady, D.G.Fox III, D.Lukacs, C.M.Lorimer, D.D.Horanyi, P.S.Edwards, T.E.Abendroth, J.

To be published.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Dihydrofolate reductase187Homo sapiensMutation(s): 0 
Gene Names: DHFR
EC: 1.5.1.3
UniProt & NIH Common Fund Data Resources
Find proteins for P00374 (Homo sapiens)
Explore P00374 
Go to UniProtKB:  P00374
PHAROS:  P00374
GTEx:  ENSG00000228716 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP00374
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAP
Query on NAP

Download Ideal Coordinates CCD File 
B [auth A]NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
C21 H28 N7 O17 P3
XJLXINKUBYWONI-NNYOXOHSSA-N
I6J
Query on I6J

Download Ideal Coordinates CCD File 
D [auth A](2S)-2-[(2-{3-[(2,4-diamino-6-ethylpyrimidin-5-yl)oxy]propoxy}phenyl)methyl]-3,3-difluoropropanoic acid
C19 H24 F2 N4 O4
UXIGBQRLXSDLOT-GFCCVEGCSA-N
HJI (Subject of Investigation/LOI)
Query on HJI

Download Ideal Coordinates CCD File 
C [auth A](2R)-2-[(2-{3-[(2,4-diamino-6-ethylpyrimidin-5-yl)oxy]propoxy}phenyl)methyl]-3,3-difluoropropanoic acid
C19 H24 F2 N4 O4
UXIGBQRLXSDLOT-LBPRGKRZSA-N
SO4
Query on SO4

Download Ideal Coordinates CCD File 
E [auth A],
F [auth A]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
CL
Query on CL

Download Ideal Coordinates CCD File 
G [auth A]CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.05 Å
  • R-Value Free: 0.180 
  • R-Value Work: 0.162 
  • R-Value Observed: 0.163 
  • Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 73.85α = 90
b = 73.85β = 90
c = 143.97γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
PDB_EXTRACTdata extraction
PHENIXmodel building
Cootmodel building
PHENIXphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesHHSN272201700059C

Revision History  (Full details and data files)

  • Version 1.0: 2022-02-09
    Type: Initial release
  • Version 1.1: 2022-03-02
    Changes: Other, Structure summary
  • Version 1.2: 2024-05-22
    Changes: Data collection