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(-) Description

Title :  THE CRYSTAL STRUCTURE OF A MUTANT NAMPT (S165F) IN COMPLEX WITH GNE-618
 
Authors :  A. Oh, M. Coons, B. Brillantes, W. Wang
Date :  15 Dec 13  (Deposition) - 22 Oct 14  (Release) - 22 Oct 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.80
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Transferase-Transferase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  W. Wang, K. Elkins, A. Oh, Y. C. Ho, J. Wu, H. Li, Y. Xiao, M. Kwong, M. Coons, B. Brillantes, E. Cheng, L. Crocker, P. S. Dragovich, D. Sampath, X. Zheng, K. W. Bair, T. O'Brien, L. D. Belmont
Structural Basis For Resistance To Diverse Classes Of Nampt Inhibitors.
Plos One V. 9 09366 2014
PubMed-ID: 25285661  |  Reference-DOI: 10.1371/JOURNAL.PONE.0109366

(-) Compounds

Molecule 1 - NICOTINAMIDE PHOSPHORIBOSYLTRANSFERASE
    ChainsA, B
    EC Number2.4.2.12
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System Taxid562
    GeneNAMPT, PBEF, PBEF1
    MutationYES
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymNAMPRTASE, NAMPT, PRE-B-CELL COLONY-ENHANCING FACTOR 1, PRE- B CELL-ENHANCING FACTOR, VISFATIN

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 9)

Asymmetric/Biological Unit (3, 9)
No.NameCountTypeFull Name
12P12Ligand/IonN-(4-{[3-(TRIFLUOROMETHYL)PHENYL]SULFONYL}BENZYL)-2H-PYRAZOLO[3,4-B]PYRIDINE-5-CARBOXAMIDE
2EDO3Ligand/Ion1,2-ETHANEDIOL
3PO44Ligand/IonPHOSPHATE ION

(-) Sites  (9, 9)

Asymmetric Unit (9, 9)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETYR A:188 , HIS A:191 , PHE A:193 , ARG A:196 , GLY A:217 , ASP A:219 , TYR A:240 , SER A:241 , VAL A:242 , ALA A:244 , SER A:275 , ILE A:309 , ARG A:311 , ILE A:351 , HOH A:815 , HOH A:876 , ASP B:16 , TYR B:18BINDING SITE FOR RESIDUE 2P1 A 601
2AC2SOFTWAREARG A:196 , GLU A:246 , HIS A:247 , ARG A:311 , ASP A:313 , HOH A:781 , TYR B:18 , HOH B:734 , HOH B:863BINDING SITE FOR RESIDUE PO4 A 602
3AC3SOFTWAREARG A:40 , ARG A:392 , SER A:398 , LYS A:400 , HOH A:747 , HOH A:795 , HOH A:814 , HOH A:1003BINDING SITE FOR RESIDUE PO4 A 603
4AC4SOFTWAREASP A:192 , GLY A:194 , TYR A:195 , VAL A:198 , ALA A:204 , GLY A:207 , ALA A:208 , THR A:220 , HOH A:997BINDING SITE FOR RESIDUE EDO A 604
5AC5SOFTWARETYR A:18 , TYR B:188 , HIS B:191 , PHE B:193 , ARG B:196 , GLY B:217 , ASP B:219 , TYR B:240 , SER B:241 , VAL B:242 , ALA B:244 , ARG B:311 , ILE B:351 , HOH B:835 , HOH B:845 , HOH B:1041BINDING SITE FOR RESIDUE 2P1 B 601
6AC6SOFTWAREARG B:40 , ARG B:392 , SER B:398 , LYS B:400 , HOH B:756 , HOH B:863 , HOH B:1206 , HOH B:1208BINDING SITE FOR RESIDUE PO4 B 602
7AC7SOFTWARETYR A:18 , HOH A:732 , HOH A:795 , ARG B:196 , GLU B:246 , HIS B:247 , ARG B:311 , ASP B:313 , HOH B:740 , HOH B:1155BINDING SITE FOR RESIDUE PO4 B 603
8AC8SOFTWARELYS A:400 , CYS A:401 , PHE A:414 , SER A:425 , HIS B:247 , SER B:248 , THR B:251 , HOH B:742BINDING SITE FOR RESIDUE EDO B 604
9AC9SOFTWAREASP B:192 , GLY B:194 , TYR B:195 , VAL B:198 , ALA B:204 , GLY B:207 , ALA B:208 , THR B:220 , HOH B:1021BINDING SITE FOR RESIDUE EDO B 605

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4O15)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4O15)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4O15)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4O15)

(-) Exons   (0, 0)

(no "Exon" information available for 4O15)

(-) 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:465
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhh.hhhhhhhhhh....eeeeeeeeee.......eee..hhhhhhhhhh.....hhhhhhhhhhhhhhhhh....hhhhhhhhhhhhh....eeeee.....eee...eeeeeee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhh.eee.hhhhh.hhhhhhhhhhhhh........hhhhhhhhhhh..............hhhhhhhhhhhhhhhhhhhhhhhh....eeee....hhhhhhhh.....hhhhhh.......eeee....hhhhhhhhhhhhhhhhh..ee.....ee....eeeee....hhhhhhhhhhhhhhh..hhh.eeeee........eeeeeeeeee..eeee.......hhhhh......eeee.....eeee..hhhhhh.......eeeee..ee....hhhhhhhhh.hhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4o15 A   8 EFNILLATDSYKVTHYKQYPPNTSKVYSYFECREKKKYEETVFYGLQYILNKYLKGKVVTKEKIQEAKDVYKEHFQDDVFNEKGWNYILEKYDGHLPIEIKAVPEGFVIPRGNVLFTVENTDPECYWLTNWIETILVQSWYPITVATNFREQKKILAKYLLETSGNLDGLEYKLHDFGYRGVSSQETAGIGASAHLVNFKGTDTVAGLALIKKYYGTKDPVPGYSVPAAEHSTITAWGKDHEKDAFEHIVTQFSSVPVSVVSDSYDIYNACEKIWGEDLRHLIVSRSTQAPLIIRPDSGNPLDTVLKVLEILGKKFPVTENSKGYKLLPPYLRVIQGDGVDINTLQEIVEGMKQKMWSIENIAFGSKLTRDLLNCSFKCSYVVTNGLGINVFKDPVADPNKRSKKGRLSLHRTPAGNFVTLEEGKGDLEEYGQDLLHTVFKNGKVTKSYSFDEIRKNAQLNIELE 487
                                    17        27        37     || 56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       336       346       356       366       376     ||392       402       412       422       432       442       452       462       472       482     
                                                              43|                                                                                                                                                                                                                                                                                                                                      382|                                                                                                  
                                                               53                                                                                                                                                                                                                                                                                                                                       389                                                                                                  

Chain B from PDB  Type:PROTEIN  Length:466
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhh.hhhhhhhhhh....eeeeeeeeee......eee..hhhhhhhhhh.....hhhhhhhhhhhhhhhh.....hhhhhhhhhhhhh....eeeee.....eee...eeeeeee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhh.eee.hhhhh.hhhhhhhhhhhhh........hhhhhhhhhhh..............hhhhhhhhhhhhhhhhhhhhhhhh....eeee....hhhhhhhh.....hhhhhh.......eeee....hhhhhhhhhhhhhhhhh..ee.....ee....eeeee....hhhhhhhhhhhhhhh..hhh.eeeee..........eeeeeeeeee..eeee.......hhhhh......eeee.....eeee..hhhhhh.......eeeee..ee....hhhhhhhhh.hhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4o15 B   8 EFNILLATDSYKVTHYKQYPPNTSKVYSYFECREKKYEETVFYGLQYILNKYLKGKVVTKEKIQEAKDVYKEHFQDDVFNEKGWNYILEKYDGHLPIEIKAVPEGFVIPRGNVLFTVENTDPECYWLTNWIETILVQSWYPITVATNFREQKKILAKYLLETSGNLDGLEYKLHDFGYRGVSSQETAGIGASAHLVNFKGTDTVAGLALIKKYYGTKDPVPGYSVPAAEHSTITAWGKDHEKDAFEHIVTQFSSVPVSVVSDSYDIYNACEKIWGEDLRHLIVSRSTQAPLIIRPDSGNPLDTVLKVLEILGKKFPVTENSKGYKLLPPYLRVIQGDGVDINTLQEIVEGMKQKMWSIENIAFGSGQKLTRDLLNCSFKCSYVVTNGLGINVFKDPVADPNKRSKKGRLSLHRTPAGNFVTLEEGKGDLEEYGQDLLHTVFKNGKVTKSYSFDEIRKNAQLNIELE 487
                                    17        27        37    ||  57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337       347       357       367       377     ||391       401       411       421       431       441       451       461       471       481      
                                                             42|                                                                                                                                                                                                                                                                                                                                       383|                                                                                                   
                                                              53                                                                                                                                                                                                                                                                                                                                        388                                                                                                   

   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  (0, 0)

(no "SCOP Domain" information available for 4O15)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4O15)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4O15)

(-) Gene Ontology  (32, 32)

Asymmetric/Biological Unit(hide GO term definitions)

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 Related Entries

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

UniProtKB/Swiss-Prot
        NAMPT_HUMAN | P434902e5b 2e5c 2e5d 2gvg 2gvj 3dgr 3dhd 3dhf 3dkj 3dkl 4jnm 4jr5 4kfn 4kfo 4kfp 4l4l 4l4m 4lts 4lv9 4lva 4lvb 4lvd 4lvf 4lvg 4lww 4m6p 4m6q 4n9b 4n9c 4n9d 4n9e 4o0z 4o10 4o12 4o13 4o14 4o16 4o17 4o18 4o19 4o1a 4o1b 4o1c 4o1d 4o28 4wq6 5kit 5u2m 5u2n 5upe 5upf

(-) Related Entries Specified in the PDB File

4o13 4o14 4o16 4o17 4o18 4o19 4o1a 4o1b 4o1c 4o1d 4o28