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(-) Description

Title :  CANDIDA GLABRATA DIHYDROFOLATE REDUCTASE COMPLEXED WITH NADPH AND 5-[3-(2-METHOXY-4-PHENYLPHENYL)BUT-1-YN-1-YL]-6-METHYLPYRIMIDINE-2,4-DIAMINE (UCP111H)
 
Authors :  J. L. Paulsen, A. C. Anderson
Date :  22 Oct 12  (Deposition) - 19 Mar 14  (Release) - 09 Apr 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Antifungal Agents, Candida Glabrata, Drug Design, Enzyme Inhibitors, Fungal Proteins, Structure-Activity Relationship, Tetrahydrofolate Dehydrogenase, Oxidoreductase-Oxidoreductase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  N. G-Dayanandan, J. L. Paulsen, K. Viswanathan, S. Keshipeddy, M. N. Lombardo, W. Zhou, K. M. Lamb, A. E. Sochia, J. B. Alverson, N. D. Priestley, D. L. Wright, A. C. Anderson
Propargyl-Linked Antifolates Are Dual Inhibitors Of Candida Albicans And Candida Glabrata.
J. Med. Chem. V. 57 2643 2014
PubMed-ID: 24568657  |  Reference-DOI: 10.1021/JM401916J

(-) Compounds

Molecule 1 - DIHYDROFOLATE REDUCTASE
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET41
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: CAGL0J03894G, DHFR
    Organism Common: YEAST
    Organism Scientific: CANDIDA GLABRATA CBS 138
    Organism Taxid: 284593
    Strain: ATCC 2001 / CBS 138 / JCM 3761 / NBRC 0622 / NRRL Y-65
    Synonym: STRAIN CBS138 CHROMOSOME J COMPLETE SEQUENCE

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (1x): A 
Biological Unit 2 (1x):  B

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 8)

Asymmetric Unit (3, 8)
No.NameCountTypeFull Name
118H2Ligand/Ion5-[3-(2-METHOXY-4-PHENYLPHENYL)BUT-1-YN-1-YL]-6-METHYLPYRIMIDINE-2,4-DIAMINE
2CL4Ligand/IonCHLORIDE ION
3NDP2Ligand/IonNADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDEPHOSPHATE
Biological Unit 1 (2, 2)
No.NameCountTypeFull Name
118H1Ligand/Ion5-[3-(2-METHOXY-4-PHENYLPHENYL)BUT-1-YN-1-YL]-6-METHYLPYRIMIDINE-2,4-DIAMINE
2CL-1Ligand/IonCHLORIDE ION
3NDP1Ligand/IonNADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDEPHOSPHATE
Biological Unit 2 (2, 2)
No.NameCountTypeFull Name
118H1Ligand/Ion5-[3-(2-METHOXY-4-PHENYLPHENYL)BUT-1-YN-1-YL]-6-METHYLPYRIMIDINE-2,4-DIAMINE
2CL-1Ligand/IonCHLORIDE ION
3NDP1Ligand/IonNADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDEPHOSPHATE

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREVAL A:10 , ALA A:11 , ILE A:19 , GLY A:20 , PHE A:21 , GLY A:23 , ASN A:24 , LEU A:25 , GLY A:55 , ARG A:56 , LYS A:57 , THR A:58 , VAL A:77 , SER A:78 , ARG A:79 , ASN A:96 , SER A:97 , LEU A:98 , ILE A:121 , GLY A:123 , GLY A:124 , GLU A:125 , ILE A:126 , TYR A:127 , GLN A:129 , 18H A:302 , CL A:304 , HOH A:410 , HOH A:427 , HOH A:454 , HOH A:484BINDING SITE FOR RESIDUE NDP A 301
2AC2SOFTWAREILE A:9 , VAL A:10 , ALA A:11 , GLU A:32 , MET A:33 , PHE A:36 , THR A:58 , SER A:61 , PRO A:63 , PHE A:66 , ILE A:121 , TYR A:127 , THR A:140 , NDP A:301 , HOH A:427BINDING SITE FOR RESIDUE 18H A 302
3AC3SOFTWAREARG A:79 , SER B:97 , LEU B:98 , ARG B:99 , NDP B:301BINDING SITE FOR RESIDUE CL A 303
4AC4SOFTWARESER A:97 , LEU A:98 , ARG A:99 , NDP A:301 , ARG B:79BINDING SITE FOR RESIDUE CL A 304
5AC5SOFTWAREARG A:37 , ARG A:72BINDING SITE FOR RESIDUE CL A 305
6AC6SOFTWARECL A:303 , VAL B:10 , ALA B:11 , ILE B:19 , GLY B:20 , GLY B:23 , ASN B:24 , LEU B:25 , GLY B:55 , ARG B:56 , LYS B:57 , THR B:58 , VAL B:77 , SER B:78 , ARG B:79 , ASN B:96 , SER B:97 , LEU B:98 , ILE B:121 , GLY B:122 , GLY B:123 , GLY B:124 , GLU B:125 , ILE B:126 , TYR B:127 , GLN B:129 , 18H B:302 , HOH B:412 , HOH B:413 , HOH B:444 , HOH B:474BINDING SITE FOR RESIDUE NDP B 301
7AC7SOFTWAREILE B:9 , VAL B:10 , ALA B:11 , ARG B:28 , GLU B:32 , MET B:33 , PHE B:36 , ILE B:62 , PRO B:63 , ILE B:121 , TYR B:127 , THR B:140 , NDP B:301BINDING SITE FOR RESIDUE 18H B 302
8AC8SOFTWAREARG B:37 , ARG B:72BINDING SITE FOR RESIDUE CL B 303

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4HOG)

(-) Cis Peptide Bonds  (6, 6)

Asymmetric Unit
No.Residues
1Leu A:14 -Pro A:15
2Arg A:67 -Pro A:68
3Gly A:122 -Gly A:123
4Leu B:14 -Pro B:15
5Arg B:67 -Pro B:68
6Gly B:122 -Gly B:123

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4HOG)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4HOG)

(-) Exons   (0, 0)

(no "Exon" information available for 4HOG)

(-) Sequences/Alignments

Asymmetric Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
  Number of residues per labelling interval =   
  UniProt sequence: complete  aligned part    
   Show mapping: SCOP domains CATH domains Pfam domains Secondary structure (by author)
SAPs(SNPs) PROSITE motifs Exons
(details for a mapped element are shown in a popup box when the mouse pointer rests over it) 
Chain A from PDB  Type:PROTEIN  Length:225
                                                                                                                                                                                                                                                                 
               SCOP domains d4hoga_ A: Dihydrofolate reductases, eukaryotic type                                                                                                                                                                              SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeeee....eee........hhhhhhhhhhhhhh......eeeeeeehhhhh............eeeee........eeee..eeee.hhhhhhhhhhhhhhhh..eeeeee..hhhhhhhhh....eeeeeeeee..........ee.hhhhhhhheee...hhhhhh..........eeeee..eeeeeeeeee..eeeeeeeeee........... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4hog A   3 KVPVVGIVAALLPEMGIGFQGNLPWRLAKEMKYFREVTTLTNDNSKQNVVIMGRKTWESIPQKFRPLPKRINVVVSRSFDGELRKVEDGIYHSNSLRNCLTALQSSLANENKIERIYIIGGGEIYRQSMDLADHWLITKIMPLPETTIPQMDTFLQKQELEQRFYDNSDKLVDFLPSSIQLEGRLTSQEWNGELVKGLPVQEKGYQFYFTLYTKKLEHHHHHHHH 227
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222     


Chain B from PDB  Type:PROTEIN  Length:225
                                                                                                                                                                                                                                                                 
               SCOP domains d4hogb_ B: Dihydrofolate reductases, eukaryotic type                                                                                                                                                                              SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeeee....eee........hhhhhhhhhhhhhh......eeeeeeehhhhh............eeeee........eeee..eeee.hhhhhhhhhhhhhhhh..eeeeee..hhhhhhhhh....eeeeeeeee..........ee.hhhhhhhheee...hhhhhh..........eeeee..eeeeeeeeee..eeeeeeeeee........... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4hog B   3 KVPVVGIVAALLPEMGIGFQGNLPWRLAKEMKYFREVTTLTNDNSKQNVVIMGRKTWESIPQKFRPLPKRINVVVSRSFDGELRKVEDGIYHSNSLRNCLTALQSSLANENKIERIYIIGGGEIYRQSMDLADHWLITKIMPLPETTIPQMDTFLQKQELEQRFYDNSDKLVDFLPSSIQLEGRLTSQEWNGELVKGLPVQEKGYQFYFTLYTKKLEHHHHHHHH 227
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222
   Legend:   → Mismatch (orange background)
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  x → Chemical Group (purple background, 'x', labelled with number + name, e.g. ACE or NH2)
  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (1, 2)

Asymmetric Unit
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4HOG)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4HOG)

(-) Gene Ontology  (10, 10)

Asymmetric Unit(hide GO term definitions)

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        Q6FPH0_CANGA | Q6FPH0: 3cse 3eej 3eek 3eel 3eem 3qlx 3qly 3qlz 3ro9 3roa 4h98

(-) Related Entries Specified in the PDB File

3qlr CANDIDA ALBICANS DIHYDROFOLATE REDUCTASE COMPLEXED WITH NADPH AND 6-METHYL-5-[(3R)-3-(3,4,5-TRIMETHOXYPHENYL)PENT- 1-YN-1-YL]PYRIMIDINE-2,4-DIAMINE (UCP112A)
3qls CANDIDA ALBICANS DIHYDROFOLATE REDUCTASE COMPLEXED WITH NADPH AND 6-METHYL-5-[3-METHYL-3-(3,4,5-TRIMETHOXYPHENYL) BUT-1-YN-1-YL]PYRIMIDINE-2,4-DIAMINE (UCP115A)
3qlw CANDIDA ALBICANS DIHYDROFOLATE REDUCTASE COMPLEXED WITH NADPH AND 5-[3-(2,5-DIMETHOXYPHENYL)PROP-1-YN-1-YL]-6- ETHYLPYRIMIDINE-2,4-DIAMINE (UCP120B)
4h95 CANDIDA ALBICANS DIHYDROFOLATE REDUCTASE COMPLEXED WITH NADPH AND 6-ETHYL-5-{3-[3-METHOXY-5-(PYRIDIN-4-YL)PHENYL] BUT-1-YN-1-YL}PYRIMIDINE-2,4-DIAMINE (UCP1006)
4h96 CANDIDA ALBICANS DIHYDROFOLATE REDUCTASE COMPLEXED WITH NADPH AND 5-{3-[3-(2,3-DIHYDRO-1,4-BENZODIOXIN-6-YL)-5- METHOXYPHENYL]PROP-1-YN-1-YL}-6-ETHYLPYRIMIDINE-2,4-DIAMINE (UCP1018)
4h97 CANDIDA ALBICANS DIHYDROFOLATE REDUCTASE COMPLEXED WITH NADPH AND 5-{3-[3-METHOXY-5-(4-METHYLPHENYL)PHENYL]BUT-1-YN -1-YL}-6-METHYLPYRIMIDINE-2,4-DIAMINE (UCP111D4M)
4h98 CANDIDA GLABRATA DIHYDROFOLATE REDUCTASE COMPLEXED WITH NADPH AND 5-{3-[3-(2,3-DIHYDRO-1,4-BENZODIOXIN-6-YL)-5- METHOXYPHENYL]PROP-1-YN-1-YL}-6-ETHYLPYRIMIDINE-2,4-DIAMINE (UCP1018)
4hoe CANDIDA ALBICANS DIHYDROFOLATE REDUCTASE COMPLEXED WITH NADPH AND 5-[3-(2,5-DIMETHOXY-4-PHENYLPHENYL)BUT-1-YN-1-YL] -6-METHYLPYRIMIDINE-2,4-DIAMINE (UCP111E)
4hof CANDIDA ALBICANS DIHYDROFOLATE REDUCTASE COMPLEXED WITH NADPH AND 5-[3-(2-METHOXY-4-PHENYLPHENYL)BUT-1-YN-1-YL]-6- METHYLPYRIMIDINE-2,4-DIAMINE