1PD8

Analysis of Three Crystal Structure Determinations of a 5-Methyl-6-N-Methylanilino Pyridopyrimidine Antifolate Complex with Human Dihydrofolate Reductase


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.197 
  • R-Value Work: 0.173 
  • R-Value Observed: 0.197 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Analysis of three crystal structure determinations of a 5-methyl-6-N-methylanilino pyridopyrimidine antifolate complex with human dihydrofolate reductase.

Cody, V.Luft, J.R.Pangborn, W.Gangjee, A.

(2003) Acta Crystallogr D Biol Crystallogr 59: 1603-1609

  • DOI: 10.1107/s0907444903014963
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • Structural data are reported for the first example of the potent antifolate inhibitor 2,4-diamino-5-methyl-6-[(3',4',5'-trimethoxy-N-methylanilino)methyl]pyrido[2,3-d]pyrimidine (1) in complex with human dihydrofolate reductase (hDHFR) and NADPH. Sma ...

    Structural data are reported for the first example of the potent antifolate inhibitor 2,4-diamino-5-methyl-6-[(3',4',5'-trimethoxy-N-methylanilino)methyl]pyrido[2,3-d]pyrimidine (1) in complex with human dihydrofolate reductase (hDHFR) and NADPH. Small differences in crystallization conditions resulted in the growth of two different forms of a binary complex. The structure determination of an additional crystal of a ternary complex of hDHFR with NADPH and (1) grown under similar conditions is also reported. Diffraction data were collected to 2.1 A resolution for an R3 lattice from a hDHFR ternary complex with NADPH and (1) and to 2.2 A resolution from a binary complex. Data were also collected to 2.1 A resolution from a binary complex with hDHFR and (1) in the first example of a tetragonal P4(3)2(1)2 lattice. Comparison of the intermolecular contacts among these structures reveals differences in the backbone conformation (1.9-3.2 A) for flexible loop regions (residues 40-46, 77-83 and 103-107) that reflect differences in the packing environment between the rhombohedral and tetragonal space groups. Analysis of the packing environments shows that the tetragonal lattice is more tightly packed, as reflected in its smaller V(M) value and lower solvent content. The conformation of the inhibitor (1) is similar in all structures and is also similar to that observed for TMQ, the parent quinazoline compound. The activity profile for this series of 5-deaza N-substituted non-classical trimethoxybenzyl antifolates shows that the N10-CH(3) substituted (1) has the greatest potency and selectivity for Toxoplasma gondii DHFR (tgDHFR) compared with its N-H or N-CHO analogs. Models of the tgDHFR active site indicate preferential contacts with (1) that are not present in either the human or Pneumocystis carinii DHFR structures. Differences in the acidic residue (Glu30 versus Asp for tgDHFR) affect the precise positioning of the diaminopyridopyrimidine ring, while changes in other residues, particularly at positions 60 and 64 (Leu versus Met and Asn versus Phe), involve interactions with the trimethoxybenzyl substituents.


    Organizational Affiliation

    Structural Biology Department, Hauptman-Woodward Medical Research Institute Inc., 73 High Street, Buffalo, NY 14203, USA. cody@hwi.buffalo.edu



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Dihydrofolate reductaseA186Homo sapiensMutation(s): 0 
Gene Names: DHFR
EC: 1.5.1.3
Find proteins for P00374 (Homo sapiens)
Explore P00374 
Go to UniProtKB:  P00374
NIH Common Fund Data Resources
PHAROS  P00374
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NDP
Query on NDP

Download CCD File 
A
NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
C21 H30 N7 O17 P3
ACFIXJIJDZMPPO-NNYOXOHSSA-N
 Ligand Interaction
CO4
Query on CO4

Download CCD File 
A
2,4-DIAMINO-5-METHYL-6-[(3,4,5-TRIMETHOXY-N-METHYLANILINO)METHYL]PYRIDO[2,3-D]PYRIMIDINE
C19 H24 N6 O3
PEGMMEYCSOZKIT-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
CO4IC50:  7.599999904632568   nM  BindingDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.197 
  • R-Value Work: 0.173 
  • R-Value Observed: 0.197 
  • Space Group: H 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 85.873α = 90
b = 85.873β = 90
c = 77.637γ = 120
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
PROTEINmodel building
PROLSQrefinement
PROTEINphasing

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2003-12-09
    Type: Initial release
  • Version 1.1: 2008-04-29
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance