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PDBsum entry 3l3r

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protein ligands links
Oxidoreductase PDB id
3l3r
Jmol
Contents
Protein chain
186 a.a. *
Ligands
OAG
NDP
SO4
Waters ×189
* Residue conservation analysis
PDB id:
3l3r
Name: Oxidoreductase
Title: Structural, computational and kinetic data for antifolate in against pneumocystis jirovecii, pneumocystis carinii and hu dihydrofolate reductase and their active site mutants
Structure: Dihydrofolate reductase. Chain: a. Engineered: yes. Mutation: yes
Source: Homo sapiens. Organism_taxid: 9606. Expressed in: escherichia coli. Expression_system_taxid: 562.
Resolution:
2.00Å     R-factor:   0.175     R-free:   0.257
Authors: V.Cody
Key ref: V.Cody et al. (2013). Kinetic and structural analysis for potent antifolate inhibition of Pneumocystis jirovecii, Pneumocystis carinii, and human dihydrofolate reductases and their active-site variants. Antimicrob Agents Chemother, 57, 2669-2677. PubMed id: 23545530 DOI: 10.1128/AAC.00172-13
Date:
17-Dec-09     Release date:   05-Jan-11    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P00374  (DYR_HUMAN) -  Dihydrofolate reductase
Seq:
Struc:
187 a.a.
186 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 1 residue position (black cross)

 Enzyme reactions 
   Enzyme class: E.C.1.5.1.3  - Dihydrofolate reductase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]

      Pathway:
Folate Coenzymes
      Reaction: 5,6,7,8-tetrahydrofolate + NADP+ = 7,8-dihydrofolate + NADPH
5,6,7,8-tetrahydrofolate
Bound ligand (Het Group name = OAG)
matches with 50.00% similarity
+
NADP(+)
Bound ligand (Het Group name = NDP)
corresponds exactly
= 7,8-dihydrofolate
+ NADPH
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     cellular_component   3 terms 
  Biological process     small molecule metabolic process   16 terms 
  Biochemical function     drug binding     6 terms  

 

 
    reference    
 
 
DOI no: 10.1128/AAC.00172-13 Antimicrob Agents Chemother 57:2669-2677 (2013)
PubMed id: 23545530  
 
 
Kinetic and structural analysis for potent antifolate inhibition of Pneumocystis jirovecii, Pneumocystis carinii, and human dihydrofolate reductases and their active-site variants.
V.Cody, J.Pace, S.F.Queener, O.O.Adair, A.Gangjee.
 
  ABSTRACT  
 
A major concern of immunocompromised patients, in particular those with AIDS, is susceptibility to infection caused by opportunistic pathogens such as Pneumocystis jirovecii, which is a leading cause of pneumonia in immunocompromised patients. We report the first kinetic and structural data for 2,4-diamino-6-[(2',5'-dichloro anilino)methyl]pyrido[2,3-d]pyrimidine (OAAG324), a potent inhibitor of dihydrofolate reductase (DHFR) from P. jirovecii (pjDHFR), and also for trimethoprim (TMP) and methotrexate (MTX) with pjDHFR, Pneumocystis carinii DHFR (pcDHFR), and human DHFR (hDHFR). OAAG324 shows a 9.0-fold selectivity for pjDHFR (Ki, 2.7 nM) compared to its selectivity for hDHFR (Ki, 24.4 nM), whereas there is only a 2.3-fold selectivity for pcDHFR (Ki, 6.3 nM). In order to understand the determinants of inhibitory potency, active-site mutations of pj-, pc-, and hDHFR were explored to make these enzymes more like each other. The most unexpected observations were that the variant pcDHFR forms with K37Q and K37Q/F69N mutations, which made the enzyme more like the human form, also made these enzymes more sensitive to the inhibitory activity of OAAG324, with Ki values of 0.26 and 0.71 nM, respectively. A similar gain in sensitivity was also observed for the hDHFR N64F variant, which showed a lower Ki value (0.58 nM) than native hDHFR, pcDHFR, or pjDHFR. Structural data are reported for complexes of OAAG324 with hDHFR and its Q35K and Q35S/N64F variants and for the complex of the K37S/F69N variant of pcDHFR with TMP. These results provide useful insight into the role of these residues in the optimization of highly selective inhibitors of DHFR against the opportunistic pathogen P. jirovecii.