5HVB | pdb_00005hvb

5-methyl-6-(1-naphthylthio)thieno[2,3-d]pyrimidine 2,4-diamine

• PDB DOI: https://doi.org/10.2210/pdb5HVB/pdb

• Classification: oxidoreductase/oxidoreductase inhibitor
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2016-01-28 Released: 2017-02-01 
• Deposition Author(s): Cody, V.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free: 
  0.263 (Depositor), 0.260 (DCC) 
• R-Value Work: 
  0.221 (Depositor), 0.220 (DCC) 
• R-Value Observed: 
  0.223 (Depositor) 

Starting Model: experimental

Literature

Human dihydrofolate reductase ternary complex with a series of fluorine substituted 5-methyl-6-(1-napthylthio)[2,3-d]pyrimidine-2,4-diamines

Cody, V., Gangjee, A.

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)

Macromolecule Content 

• Total Structure Weight: 22.43 kDa 
• Atom Count: 1,624 
• Modeled Residue Count: 186 
• Deposited Residue Count: 186 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Dihydrofolate reductase	A	186	Homo sapiens	Mutation(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

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NDP	C [auth A]	NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE C21 H30 N7 O17 P3 ACFIXJIJDZMPPO-NNYOXOHSSA-N
65O	B [auth A]	5-methyl-6-(naphthalen-1-ylsulfanyl)thieno[2,3-d]pyrimidine-2,4-diamine C17 H14 N4 S2 DSWPJTXRDPNDRO-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free:  0.263 (Depositor), 0.260 (DCC) 
• R-Value Work:  0.221 (Depositor), 0.220 (DCC) 
• R-Value Observed: 0.223 (Depositor) 

Space Group: H 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 85.973	α = 90
b = 85.973	β = 90
c = 76.833	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
SCALA	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2017-02-01 
Deposition Author(s): Cody, V.

Revision History  

• Version 1.0: 2017-02-01
  Type: Initial release
  
• Version 1.1: 2017-09-27
  Changes: Author supporting evidence
• Version 1.2: 2023-09-27
  Changes: Data collection, Database references, Refinement description