2W3B | pdb_00002w3b

HUMAN DIHYDROFOLATE REDUCTASE COMPLEXED WITH NADPH AND A LIPOPHILIC ANTIFOLATE SELECTIVE FOR MYCOBACTERIUM AVIUM DHFR, 6-((2,5- DIETHOXYPHENYL)AMINOMETHYL)-2,4-DIAMINO-5-METHYLPYRIDO(2,3-D) PYRIMIDINE (SRI-8686)

• PDB DOI: https://doi.org/10.2210/pdb2W3B/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2008-11-11 Released: 2009-11-17 
• Deposition Author(s): Leung, A.K.W., Reynolds, R.C., Borhani, D.W.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.27 Å
• R-Value Free: 
  0.203 (Depositor), 0.250 (DCC) 
• R-Value Work: 
  0.171 (Depositor), 0.220 (DCC) 
• R-Value Observed: 
  0.172 (Depositor) 

Starting Model: other

Literature

Structural Basis for Selective Inhibition of Mycobacterium Avium Dihydrofolate Reductase by a Lipophilic Antifolate

Leung, A.K.W., Ross, L.J., Zywno-Van Ginkel, S., Reynolds, R.C., Seitz, L.E., Pathak, V., Barrow, W.W., White, E.L., Suling, W.J., Piper, J.R., Borhani, D.W.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 46.15 kDa 
• Atom Count: 3,848 
• Modelled Residue Count: 371 
• Deposited Residue Count: 374 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DIHYDROFOLATE REDUCTASE	A, B	187	Homo sapiens	Mutation(s): 0  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

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NDP	C [auth A], G [auth B]	NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE C21 H30 N7 O17 P3 ACFIXJIJDZMPPO-NNYOXOHSSA-N
FOL	E [auth A], I [auth B]	FOLIC ACID C19 H19 N7 O6 OVBPIULPVIDEAO-LBPRGKRZSA-N
VG9	D [auth A], H [auth B]	6-{[(2,5-DIETHOXYPHENYL)AMINO]METHYL}-5-METHYLPYRIDO[2,3-D]PYRIMIDINE-2,4-DIAMINE C19 H24 N6 O2 KKMWDWUZXFYKLD-UHFFFAOYSA-N
K	F [auth A], J [auth B]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
VG9	BindingDB:  2W3B	IC50: min: 0.84, max: 2300 (nM) from 4 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.27 Å
• R-Value Free:  0.203 (Depositor), 0.250 (DCC) 
• R-Value Work:  0.171 (Depositor), 0.220 (DCC) 
• R-Value Observed: 0.172 (Depositor) 

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 87.725	α = 90
b = 94.387	β = 90
c = 95.439	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling
AMoRE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-11-17 
Deposition Author(s): Leung, A.K.W., Reynolds, R.C., Borhani, D.W.

Revision History  

• Version 1.0: 2009-11-17
  Type: Initial release
  
• Version 1.1: 2011-05-08
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2019-03-06
  Changes: Data collection, Experimental preparation, Other
• Version 1.4: 2019-05-08
  Changes: Data collection, Experimental preparation
• Version 1.5: 2024-05-01
  Changes: Data collection, Database references, Derived calculations, Other, Refinement description