1KMV

HUMAN DIHYDROFOLATE REDUCTASE COMPLEXED WITH NADPH AND (Z)-6-(2-[2,5-DIMETHOXYPHENYL]ETHEN-1-YL)-2,4-DIAMINO-5-METHYLPYRIDO[2,3-D]PYRIMIDINE (SRI-9662), A LIPOPHILIC ANTIFOLATE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.05 Å
  • R-Value Free: 0.181
  • R-Value Work: 0.130

Literature

Macromolecules
Sequence Display for 1KMV

Classification: OXIDOREDUCTASE

Total Structure Weight: 22606.52

Macromolecule Entities
Molecule Chains Length Organism Details
DIHYDROFOLATE REDUCTASE A 186 Homo sapiens EC#: 1.5.1.3 IUBMB
Gene Name(s): DHFR Gene View
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

Small Molecules
Ligands 4 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
NDP
Query on NDP

A NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
C21 H30 N7 O17 P3
ACFIXJIJDZMPPO-NNYOXOHSSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
LII
Query on LII

A (Z)-6-(2-[2,5-DIMETHOXYPHENYL]ETHEN-1-YL)- 2,4-DIAMINO-5-METHYLPYRIDO[2,3-D]PYRIMIDINE
SRI-9662 (Synonym)
C18 H19 N5 O2
WNDJHUNKXPAREB-PLNGDYQASA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
SO4
Query on SO4

A SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
DMS
Query on DMS

A DIMETHYL SULFOXIDE
C2 H6 O S
IAZDPXIOMUYVGZ-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
External Ligand Annotations
ID Binding Affinity (Sequence Identity %)
LII N/A in BindingDB
N/A in BindingMoad
IC50: 112 nM  PDBbind

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.05 Å
  • R-Value Free: 0.181
  • R-Value Work: 0.130
  • Space Group: P 21 21 21

Unit Cell:

Length (Å) Angle (°)
a = 41.30 α = 90.00
b = 54.99 β = 90.00
c = 82.68 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2001-12-17
  • Released Date: 2002-07-10
  • Deposition author(s): Klon, A.E., Heroux, A., Ross, L.J., Pathak, V., Johnson, C.A., Piper, J.R., Borhani, D.W.

Revision History

  • Version 1_0: 2002-07-10

    Type: Initial release

  • Version 1_1: 2008-04-27

    Type: Version format compliance

  • Version 1_2: 2011-07-13

    Type: Version format compliance