PDBsum entry 1kms

Oxidoreductase

PDB id: 1kms

Contents

Protein chain

185 a.a. *

Ligands

SO4 ×2

LIH

NDP

Waters ×399

* Residue conservation analysis

PDB id:

1kms

Name:

Oxidoreductase

Title:

Human dihydrofolate reductase complexed with NADPH and 6-([5- quinolylamino]methyl)-2,4-diamino-5-methylpyrido[2,3-d]pyrimidine (sri-9439), a lipophilic antifolate

Structure:

Dihydrofolate reductase. Chain: a. Synonym: dhfr. Engineered: yes

Source:

Homo sapiens. Human. Organism_taxid: 9606. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.

Resolution:

1.09Å R-factor: 0.131 R-free: 0.173

Authors:

A.E.Klon,A.Heroux,L.J.Ross,V.Pathak,C.A.Johnson,J.R.Piper,D.W.Borhani

Key ref:

A.E.Klon et al. (2002). Atomic structures of human dihydrofolate reductase complexed with NADPH and two lipophilic antifolates at 1.09 a and 1.05 a resolution. J Mol Biol, 320, 677-693. PubMed id: 12096917 DOI: 10.1016/S0022-2836(02)00469-2

Date:

17-Dec-01 Release date: 10-Jul-02

Protein chain

P00374  (DYR_HUMAN) -  Dihydrofolate reductase from Homo sapiens

Seq: 187 a.a.

Struc: 185 a.a.

Enzyme reactions

• Enzyme class: E.C.1.5.1.3 - dihydrofolate reductase.
• Pathway: Folate Coenzymes
• Reaction: (6S)-5,6,7,8-tetrahydrofolate + NADP⁺ = 7,8-dihydrofolate + NADPH + H⁺

(6S)-5,6,7,8-tetrahydrofolate + NADP(+) (Bound ligand (Het Group name = NDP) corresponds exactly) = 7,8-dihydrofolate (Bound ligand (Het Group name = LIH) matches with 62.86% similarity) + NADPH + H(+)

Molecule diagrams generated from .mol files obtained from the KEGG ftp site

reference

DOI no: 10.1016/S0022-2836(02)00469-2

J Mol Biol 320:677-693 (2002)

PubMed id: 12096917

Atomic structures of human dihydrofolate reductase complexed with NADPH and two lipophilic antifolates at 1.09 a and 1.05 a resolution.

A.E.Klon, A.Héroux, L.J.Ross, V.Pathak, C.A.Johnson, J.R.Piper, D.W.Borhani.

ABSTRACT

The crystal structures of two human dihydrofolate reductase (hDHFR) ternary complexes, each with bound NADPH cofactor and a lipophilic antifolate inhibitor, have been determined at atomic resolution. The potent inhibitors 6-([5-quinolylamino]methyl)-2,4-diamino-5-methylpyrido[2,3-d]pyrimidine (SRI-9439) and (Z)-6-(2-[2,5-dimethoxyphenyl]ethen-1-yl)-2,4-diamino-5-methylpyrido[2,3-d]pyrimidine (SRI-9662) were developed at Southern Research Institute against Toxoplasma gondii DHFR-thymidylate synthase. The 5-deazapteridine ring of each inhibitor adopts an unusual puckered conformation that enables the formation of identical contacts in the active site. Conversely, the quinoline and dimethoxybenzene moieties exhibit distinct binding characteristics that account for the differences in inhibitory activity. In both structures, a salt-bridge is formed between Arg70 in the active site and Glu44 from a symmetry-related molecule in the crystal lattice that mimics the binding of methotrexate to DHFR.

Selected figure(s)

Figure 3.
Figure 3. The inhibitors bind in the hDHFR active site in an unambiguous conformation. In this stereoview, rotated vert, similar 180° from the orientation of Figure 1, (a) SRI-9439 and (b) SRI-9662 are shown as found in the hDHFR/NADPH ternary complexes. The 1.5 Å resolution F[O] -F[C] electron density maps, contoured at 2.5 s, show the positive electron density in the active site prior to the addition of either inhibitor to the molecular models. Ligands are colored as before; the protein C atoms are sea-green. Selected hydrogen bonds are shown by lines (broken lines if >3.0 Å). Note especially the hydrogen bonds between the 5-deazapteridine ring and Glu30, and the distinct water-mediated hydrogen bonds to the lipophilic moieties.

Figure 5.
Figure 5. The 5-deazapteridine rings of both inhibitors pucker dramatically upon binding to hDHFR. (a) The bound conformations of both SRI-9439 (C, gray; N, blue) and SRI-9662 (C, steel-blue; N, cyan) exhibit a pronounced puckering in the 5-deazapteridine ring, which allows optimal interactions with hDHFR. Despite the conformational constraint of the cis double bond, SRI-9662 occupies a similar spatial region as SRI-9439. (b) The 5-deazapteridine ring of SRI-9439 (and SRI-9662) is much more puckered than the deazapteridine rings of unbound trimetrexate (TMQ; C, gold; N, cyan) or piritrexim (PTX; C, tan; N, cyan). (c) PTX bound to hDHFR (Leu22Phe mutant[51.]) is canted in the active site compared to SRI-9439.

The above figures are reprinted by permission from Elsevier: J Mol Biol (2002, 320, 677-693) copyright 2002.

Figures were selected by the author.