1OHJ

HUMAN DIHYDROFOLATE REDUCTASE, MONOCLINIC (P21) CRYSTAL FORM


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Work: 0.208 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Comparison of two independent crystal structures of human dihydrofolate reductase ternary complexes reduced with nicotinamide adenine dinucleotide phosphate and the very tight-binding inhibitor PT523.

Cody, V.Galitsky, N.Luft, J.R.Pangborn, W.Rosowsky, A.Blakley, R.L.

(1997) Biochemistry 36: 13897-13903

  • DOI: 10.1021/bi971711l
  • Primary Citation of Related Structures:  1OHK

  • PubMed Abstract: 
  • Structural data for two independent crystal forms (monoclinic, C2, and orthorhombic, P2(1)2(1)2(1)) of the ternary complex of the potent antitumor agent PT523 [N alpha-(4-amino-4-deoxypteroyl)-N delta-hemiphthaloyl-L-ornithine], reduced nicotinamide ...

    Structural data for two independent crystal forms (monoclinic, C2, and orthorhombic, P2(1)2(1)2(1)) of the ternary complex of the potent antitumor agent PT523 [N alpha-(4-amino-4-deoxypteroyl)-N delta-hemiphthaloyl-L-ornithine], reduced nicotinamide adenine dinucleotide phosphate (NADPH), and recombinant human dihydrofolate reductase (hDHFR) reveals multiple binding orientations for the hemiphthaloyl group of the inhibitor. Analysis of these data shows that PT523 binds with its pteridine ring in the same orientation observed for methotrexate (MTX) analogues. However, in each structure, the hemiphthaloyl ring occupies three alternate conformations. In the C2 lattice, the phthaloyl moiety binds in two extended conformations, A and C, with each conformer having a 180 degrees flip of the o-carboxylate group, and a third, lower occupancy conformer B, with the phthaloyl group folded within contact of the active-site pocket. In the orthorhombic lattice, PT523 also has three conformers for the phthaloyl group; however, these differ from those observed in the monoclinic lattice. Two major conformers, A and C, are displaced on either side of the extended position observed in the C2 lattice, one near the folded B conformer of the C2 lattice and the other extended. These conformers form tighter intermolecular contacts than those in the C2 lattice. Conformer B is folded back away from the active site in a unique position. There are also significant differences in the conformation of the adenine-ribose moiety of NADPH in both complexes that differ from that observed for other inhibitor-NADPH-hDHFR ternary complexes. These data suggest that the added intermolecular contacts made by the hemiphaloyl group of PT523 contribute to its tighter binding to hDHFR than MTX, which does not extend as far from the active site and cannot make these contacts. These crystallographic observations of multiple conformations for the hemiphthaloyl group are in general agreement with solution NMR data for the binding of PT523 to hDHFR [Johnson et al. (1997) Biochemistry 36, 4399-4411], which show that the hemiphthaloyl group may adopt more than one conformation. However, the crystallographic data reveal more discretely occupied positions than can be interpreted from the solution data. These results suggest that crystal packing interactions may influence their stability.


    Related Citations: 
    • Methotrexate-Resistant Variants of Human Dihydrofolate Reductase. Effects of Phe31 Substitutions
      Chunduru, S.K.,Cody, V.,Luft, J.R.,Pangborn, W.,Appleman, J.R.,Blakley, R.L.
      (1994) J.Biol.Chem. 269: 9547
    • Methotrexate-Resistant Variants of Human Dihydrofolate Reductase with Substitutions of Leucine 22. Kinetics, Crystallography, and Potential as Selectable Markers
      Lewis, W.S.,Cody, V.,Galitsky, N.,Luft, J.R.,Pangborn, W.,Chunduru, S.K.,Spencer, H.T.,Appleman, J.R.,Blakley, R.L.
      (1995) J.Biol.Chem. 270: 5057
    • Crystal Structure Determination at 2.3 A of Recombinant Human Dihydrofolate Reductase Ternary Complex with Nadph and Methotrexate-Gamma-Tetrazole
      Cody, V.,Luft, J.R.,Ciszak, E.,Kalman, T.I.,Freisheim, J.H.
      (1992) Anti-Cancer Drug Des. 7: 483


    Organizational Affiliation

    Hauptman-Woodward Medical Research Institute, Inc., Buffalo, New York 14203, USA. cody@hwi.buffalo.edu




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
DIHYDROFOLATE REDUCTASE
A
186Homo sapiensGene Names: DHFR
EC: 1.5.1.3
Find proteins for P00374 (Homo sapiens)
Go to Gene View: DHFR
Go to UniProtKB:  P00374
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
COP
Query on COP

Download SDF File 
Download CCD File 
A
N-(4-CARBOXY-4-{4-[(2,4-DIAMINO-PTERIDIN-6-YLMETHYL)-AMINO]-BENZOYLAMINO}-BUTYL)-PHTHALAMIC ACID
PT523
C27 H27 N9 O6
NYQPLPNEESYGNO-IBGZPJMESA-N
 Ligand Interaction
NDP
Query on NDP

Download SDF File 
Download CCD File 
A
NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
C21 H30 N7 O17 P3
ACFIXJIJDZMPPO-NNYOXOHSSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
COPKi: 0 - 25.9 nM (89) BINDINGDB
COPIC50: 1.1 - 52 nM (100) BINDINGDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Work: 0.208 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 65.822α = 90.00
b = 40.350β = 109.74
c = 75.150γ = 90.00
Software Package:
Software NamePurpose
PROFFTrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1998-04-29
    Type: Initial release
  • Version 1.1: 2008-03-03
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance