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(-) Description

Title :  HIGH THROUGHPUT SCREENING AND X-RAY CRYSTALLOGRAPHY ASSISTED EVALUATION OF SMALL MOLECULE SCAFFOLDS FOR CYP51 INHIBITORS
 
Authors :  L. M. Podust, Y. Kim, L. V. Yermalitskaya, J. P. Von Kries, M. R. Waterman
Date :  17 Mar 06  (Deposition) - 03 Jul 07  (Release) - 21 Apr 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.50
Chains :  Asym./Biol. Unit :  A
Keywords :  Heme, Heme Lipid Synthesis, Metal-Binding, Monooxygenase, Nadp, Oxidoreductase, Protein-Inhibitor Complex, Steroid Biosynthesis, Sterol Biosynthesis (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  L. M. Podust, J. P. Von Kries, A. N. Eddine, Y. Kim, L. V. Yermalitskaya, R. Kuehne, H. Ouellet, T. Warrier, M. Altekoster, J. -S. Lee, J. Rademann, H. Oschkinat, S. H. E. Kaufmann, M. R. Waterman
Small Molecule Scaffolds For Cyp51 Inhibitors Identified By High Throughput Screening And Defined By X-Ray Crystallography
Antimicrob. Agents Chemother. V. 51 3915 2007
PubMed-ID: 17846131  |  Reference-DOI: 10.1128/AAC.00311-07

(-) Compounds

Molecule 1 - CYTOCHROME P450 51
    Chains: A
    EC Number: 1.14.13.70
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET17B
    Expression System Strain: HMS174(DE3)
    Expression System Taxid: 562
    Expression System Vector: PET
    Mutation: YES
    Organism Scientific: MYCOBACTERIUM TUBERCULOSIS
    Organism Taxid: 83332
    Other Details: 4XHIS TAG AT THE C-TERMINUS
    Strain: H37RV
    Synonym: STEROL 14ALPHA-DEMETHYLASE CYP51, YPLI, P450-LIA1, STEROL 14-ALPHA DEMETHYLASE, LANOSTEROL 14-ALPHA DEMETHYLASE, P450-14DM

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 2)

Asymmetric/Biological Unit (2, 2)
No.NameCountTypeFull Name
1CM61Ligand/Ion(2S)-2-[(2,1,3-BENZOTHIADIAZOL-4-YLSULFONYL)AMINO]-2-PHENYL-N-PYRIDIN-4-YLACETAMIDE
2HEM1Ligand/IonPROTOPORPHYRIN IX CONTAINING FE

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREPHE A:63 , LEU A:105 , GLY A:257 , THR A:260 , THR A:264 , PRO A:320 , ARG A:326 , PRO A:386 , PHE A:387 , GLY A:388 , HIS A:392 , CYS A:394 , VAL A:395 , CM6 A:1450 , HOH A:2067 , HOH A:2356BINDING SITE FOR RESIDUE HEM A1449
2AC2SOFTWARETYR A:76 , MET A:79 , PHE A:83 , ALA A:256 , LEU A:321 , MET A:433 , HEM A:1449 , HOH A:2067 , HOH A:2358BINDING SITE FOR RESIDUE CM6 A1450

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2CIB)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Gln A:439 -Pro A:440

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2CIB)

(-) PROSITE Motifs  (1, 1)

Asymmetric/Biological Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1CYTOCHROME_P450PS00086 Cytochrome P450 cysteine heme-iron ligand signature.CP51_MYCTO387-396  1A:387-396
CP51_MYCTU387-396  1A:387-396

(-) Exons   (0, 0)

(no "Exon" information available for 2CIB)

(-) Sequences/Alignments

Asymmetric/Biological 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:420
 aligned with CP51_MYCTO | P9WPP8 from UniProtKB/Swiss-Prot  Length:451

    Alignment length:445
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364       374       384       394       404       414       424       434       444     
           CP51_MYCTO     5 ALPRVSGGHDEHGHLEEFRTDPIGLMQRVRDECGDVGTFQLAGKQVVLLSGSHANEFFFRAGDDDLDQAKAYPFMTPIFGEGVVFDASPERRKEMLHNAALRGEQMKGHAATIEDQVRRMIADWGEAGEIDLLDFFAELTIYTSSACLIGKKFRDQLDGRFAKLYHELERGTDPLAYVDPYLPIESFRRRDEARNGLVALVADIMNGRIANPPTDKSDRDMLDVLIAVKAETGTPRFSADEITGMFISMMFAGHHTSSGTASWTLIELMRHRDAYAAVIDELDELYGDGRSVSFHALRQIPQLENVLKETLRLHPPLIILMRVAKGEFEVQGHRIHEGDLVAASPAISNRIPEDFPDPHDFVPARYEQPRQEDLLNRWTWIPFGAGRHRCVGAAFAIMQIKAIFSVLLREYEFEMAQPPESYRNDHSKMVVQLAQPACVRYRRRT 449
               SCOP domains d2ciba_ A: automated matches                                                                                                                                                                                                                                                                                                                                                                                                                                  SCOP domains
               CATH domains 2cibA00 A:5-449 Cytochrome p450                                                                                                                                                                                                                                                                                                                                                                                                                               CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .............hhhhhh.hhhhhhhhhhhhhh.eeeeee..eeeeee.hhhhhhhhhhh....ee....hhhhhhhhh--------------------.hhhhhhhhhhhhhhhhhhhhh....eeeeehhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhh..hhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhh.-----..hhhhhhhhh.........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhh...hhhhhhhhhhhhhhh.....eeeee...eee..eee....eeeehhhhhh............hhhhhh...hhhhhh........hhhhh..hhhhhhhhhhhhhhhhhhheeeee..hhhhh.ee......ee....eeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CYTOCHROME----------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2cib A   5 ALPRVSGGHDEHGHLEEFRTDPIGLMQRVRDELGDVGTFQLAGKQVVLLSGSHANEFFFRAGDDDLDQAKAYPFMTPIFG--------------------LRGEQMKGHAATIEDQVRRMIADWGEAGEIDLLDFFAELTIYTSSACLIGKKFRDQLDGRFAKLYHELERGTDPLAYVDPYLPIESFRRRDEARNGLVALVADIMNGRIANP-----DRDMLDVLIAVKAETGTPRFSADEITGMFISMMFAGHHTSSGTASWTLIELMRHRDAYAAVIDELDELYGDGRSVSFHALRQIPQLENVLKETLRLHPPLIILMRVAKGEFEVQGHRIHEGDLVAASPAISNRIPEDFPDPHDFVPARYEQPRQEDLLNRWTWIPFGAGRHRCVGAAFAIMQIKAIFSVLLREYEFEMAQPPESYRNDHSKMVVQLAQPAAVRYRRRT 449
                                    14        24        34        44        54        64        74        84         -         -|      114       124       134       144       154       164       174       184       194       204       214 |     224       234       244       254       264       274       284       294       304       314       324       334       344       354       364       374       384       394       404       414       424       434       444     
                                                                                                          84                  105                                                                                                            216   222                                                                                                                                                                                                                                   


Chain A from PDB  Type:PROTEIN  Length:420
 aligned with CP51_MYCTU | P9WPP9 from UniProtKB/Swiss-Prot  Length:451

    Alignment length:445
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364       374       384       394       404       414       424       434       444     
           CP51_MYCTU     5 ALPRVSGGHDEHGHLEEFRTDPIGLMQRVRDECGDVGTFQLAGKQVVLLSGSHANEFFFRAGDDDLDQAKAYPFMTPIFGEGVVFDASPERRKEMLHNAALRGEQMKGHAATIEDQVRRMIADWGEAGEIDLLDFFAELTIYTSSACLIGKKFRDQLDGRFAKLYHELERGTDPLAYVDPYLPIESFRRRDEARNGLVALVADIMNGRIANPPTDKSDRDMLDVLIAVKAETGTPRFSADEITGMFISMMFAGHHTSSGTASWTLIELMRHRDAYAAVIDELDELYGDGRSVSFHALRQIPQLENVLKETLRLHPPLIILMRVAKGEFEVQGHRIHEGDLVAASPAISNRIPEDFPDPHDFVPARYEQPRQEDLLNRWTWIPFGAGRHRCVGAAFAIMQIKAIFSVLLREYEFEMAQPPESYRNDHSKMVVQLAQPACVRYRRRT 449
               SCOP domains d2ciba_ A: automated matches                                                                                                                                                                                                                                                                                                                                                                                                                                  SCOP domains
               CATH domains 2cibA00 A:5-449 Cytochrome p450                                                                                                                                                                                                                                                                                                                                                                                                                               CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .............hhhhhh.hhhhhhhhhhhhhh.eeeeee..eeeeee.hhhhhhhhhhh....ee....hhhhhhhhh--------------------.hhhhhhhhhhhhhhhhhhhhh....eeeeehhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhh..hhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhh.-----..hhhhhhhhh.........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhh...hhhhhhhhhhhhhhh.....eeeee...eee..eee....eeeehhhhhh............hhhhhh...hhhhhh........hhhhh..hhhhhhhhhhhhhhhhhhheeeee..hhhhh.ee......ee....eeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (2) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CYTOCHROME----------------------------------------------------- PROSITE (2)
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2cib A   5 ALPRVSGGHDEHGHLEEFRTDPIGLMQRVRDELGDVGTFQLAGKQVVLLSGSHANEFFFRAGDDDLDQAKAYPFMTPIFG--------------------LRGEQMKGHAATIEDQVRRMIADWGEAGEIDLLDFFAELTIYTSSACLIGKKFRDQLDGRFAKLYHELERGTDPLAYVDPYLPIESFRRRDEARNGLVALVADIMNGRIANP-----DRDMLDVLIAVKAETGTPRFSADEITGMFISMMFAGHHTSSGTASWTLIELMRHRDAYAAVIDELDELYGDGRSVSFHALRQIPQLENVLKETLRLHPPLIILMRVAKGEFEVQGHRIHEGDLVAASPAISNRIPEDFPDPHDFVPARYEQPRQEDLLNRWTWIPFGAGRHRCVGAAFAIMQIKAIFSVLLREYEFEMAQPPESYRNDHSKMVVQLAQPAAVRYRRRT 449
                                    14        24        34        44        54        64        74        84         -         -|      114       124       134       144       154       164       174       184       194       204       214 |     224       234       244       254       264       274       284       294       304       314       324       334       344       354       364       374       384       394       404       414       424       434       444     
                                                                                                          84                  105                                                                                                            216   222
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
    → Modified Residue (blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
  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, 1)

Asymmetric/Biological Unit
(-)
Class: All alpha proteins (14657)

(-) CATH Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Class: Mainly Alpha (13335)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2CIB)

(-) Gene Ontology  (17, 31)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (CP51_MYCTU | P9WPP9)
molecular function
    GO:0020037    heme binding    Interacting selectively and non-covalently with heme, any compound of iron complexed in a porphyrin (tetrapyrrole) ring.
    GO:0005506    iron ion binding    Interacting selectively and non-covalently with iron (Fe) ions.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0004497    monooxygenase activity    Catalysis of the incorporation of one atom from molecular oxygen into a compound and the reduction of the other atom of oxygen to water.
    GO:0016491    oxidoreductase activity    Catalysis of an oxidation-reduction (redox) reaction, a reversible chemical reaction in which the oxidation state of an atom or atoms within a molecule is altered. One substrate acts as a hydrogen or electron donor and becomes oxidized, while the other acts as hydrogen or electron acceptor and becomes reduced.
    GO:0016705    oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen    Catalysis of an oxidation-reduction (redox) reaction in which hydrogen or electrons are transferred from each of two donors, and molecular oxygen is reduced or incorporated into a donor.
    GO:0005515    protein binding    Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
    GO:0008398    sterol 14-demethylase activity    Catalysis of the reaction: obtusifoliol + 3 O2 + 3 NADPH + 3 H+ = 4-alpha-methyl-5-alpha-ergosta-8,14,24(28)-trien-3-beta-ol + formate + 3 NADP+ + 3 H2O.
biological process
    GO:0070988    demethylation    The process of removing one or more methyl groups from a molecule.
    GO:0006629    lipid metabolic process    The chemical reactions and pathways involving lipids, compounds soluble in an organic solvent but not, or sparingly, in an aqueous solvent. Includes fatty acids; neutral fats, other fatty-acid esters, and soaps; long-chain (fatty) alcohols and waxes; sphingoids and other long-chain bases; glycolipids, phospholipids and sphingolipids; and carotenes, polyprenols, sterols, terpenes and other isoprenoids.
    GO:0055114    oxidation-reduction process    A metabolic process that results in the removal or addition of one or more electrons to or from a substance, with or without the concomitant removal or addition of a proton or protons.
    GO:0006694    steroid biosynthetic process    The chemical reactions and pathways resulting in the formation of steroids, compounds with a 1,2,cyclopentanoperhydrophenanthrene nucleus; includes de novo formation and steroid interconversion by modification.
    GO:0008202    steroid metabolic process    The chemical reactions and pathways involving steroids, compounds with a 1,2,cyclopentanoperhydrophenanthrene nucleus.
    GO:0016126    sterol biosynthetic process    The chemical reactions and pathways resulting in the formation of sterols, steroids with one or more hydroxyl groups and a hydrocarbon side-chain in the molecule.
    GO:0016125    sterol metabolic process    The chemical reactions and pathways involving sterols, steroids with one or more hydroxyl groups and a hydrocarbon side-chain in the molecule.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0005829    cytosol    The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.

Chain A   (CP51_MYCTO | P9WPP8)
molecular function
    GO:0020037    heme binding    Interacting selectively and non-covalently with heme, any compound of iron complexed in a porphyrin (tetrapyrrole) ring.
    GO:0005506    iron ion binding    Interacting selectively and non-covalently with iron (Fe) ions.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0004497    monooxygenase activity    Catalysis of the incorporation of one atom from molecular oxygen into a compound and the reduction of the other atom of oxygen to water.
    GO:0016491    oxidoreductase activity    Catalysis of an oxidation-reduction (redox) reaction, a reversible chemical reaction in which the oxidation state of an atom or atoms within a molecule is altered. One substrate acts as a hydrogen or electron donor and becomes oxidized, while the other acts as hydrogen or electron acceptor and becomes reduced.
    GO:0016705    oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen    Catalysis of an oxidation-reduction (redox) reaction in which hydrogen or electrons are transferred from each of two donors, and molecular oxygen is reduced or incorporated into a donor.
    GO:0008398    sterol 14-demethylase activity    Catalysis of the reaction: obtusifoliol + 3 O2 + 3 NADPH + 3 H+ = 4-alpha-methyl-5-alpha-ergosta-8,14,24(28)-trien-3-beta-ol + formate + 3 NADP+ + 3 H2O.
biological process
    GO:0070988    demethylation    The process of removing one or more methyl groups from a molecule.
    GO:0006629    lipid metabolic process    The chemical reactions and pathways involving lipids, compounds soluble in an organic solvent but not, or sparingly, in an aqueous solvent. Includes fatty acids; neutral fats, other fatty-acid esters, and soaps; long-chain (fatty) alcohols and waxes; sphingoids and other long-chain bases; glycolipids, phospholipids and sphingolipids; and carotenes, polyprenols, sterols, terpenes and other isoprenoids.
    GO:0055114    oxidation-reduction process    A metabolic process that results in the removal or addition of one or more electrons to or from a substance, with or without the concomitant removal or addition of a proton or protons.
    GO:0006694    steroid biosynthetic process    The chemical reactions and pathways resulting in the formation of steroids, compounds with a 1,2,cyclopentanoperhydrophenanthrene nucleus; includes de novo formation and steroid interconversion by modification.
    GO:0008202    steroid metabolic process    The chemical reactions and pathways involving steroids, compounds with a 1,2,cyclopentanoperhydrophenanthrene nucleus.
    GO:0016126    sterol biosynthetic process    The chemical reactions and pathways resulting in the formation of sterols, steroids with one or more hydroxyl groups and a hydrocarbon side-chain in the molecule.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        CP51_MYCTO | P9WPP8: 1e9x 1ea1 1h5z 1u13 1x8v 2bz9 2ci0 2vku 2w09 2w0a 2w0b
        CP51_MYCTU | P9WPP9: 1e9x 1ea1 1h5z 1u13 1x8v 2bz9 2ci0 2vku 2w09 2w0a 2w0b

(-) Related Entries Specified in the PDB File

1e9x CYTOCHROME P450 14 ALPHA-STEROL DEMETHYLASE ( CYP51) FROM MYCOBACTERIUM TUBERCULOSIS IN COMPLEX WITH 4-PHENYLIMIDAZOLE
1ea1 CYTOCHROME P450 14 ALPHA-STEROL DEMETHYLASE ( CYP51) FROM MYCOBACTERIUM TUBERCULOSIS IN COMPLEX WITH FLUCONAZOLE
1h5z CYTOCHROME P450 14 ALPHA-STEROL DEMETHYLASE ( CYP51) FROM MYCOBACTERIUM TUBERCULOSIS IN FERRIC LOW-SPIN STATE
1u13 CRYSTAL STRUCTURE ANALYSIS OF THE C37L/C151T /C442A-TRIPLEMUTANT OF CYP51 FROM MYCOBACTERIUM TUBERCULOSIS
1x8v ESTRIOL-BOUND AND LIGAND-FREE STRUCTURES OF STEROL 14ALPHA-DEMETHYLASE (CYP51)
2bz9 LIGAND-FREE STRUCTURE OF STEROL 14ALPHA- DEMETHYLASE FROM MYCOBACTERIUM TUBERCULOSIS IN P2(1) SPACE GROUP
2ci0 HIGH THROUGHPUT SCREENING AND X-RAY CRYSTALLOGRAPHY ASSISTED EVALUATION OF SMALL MOLECULE SCAFFOLDS FOR CYP51 INHIBITORS