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(-) Description

Title :  STRUCTURAL BASIS FOR RESISTANCE TO DIVERSE CLASSES OF NAMPT INHIBITORS
 
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 :  1.78
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
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
    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

  1
Asymmetric Unit A
Biological Unit 1 (2x)A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 16)

Asymmetric Unit (3, 16)
No.NameCountTypeFull Name
11XC1Ligand/Ion6-({4-[(3,5-DIFLUOROPHENYL)SULFONYL]BENZYL}CARBAMOYL)-1-(5-O-PHOSPHONO-BETA-D-RIBOFURANOSYL)IMIDAZO[1,2-A]PYRIDIN-1-IUM
2EDO13Ligand/Ion1,2-ETHANEDIOL
3PO42Ligand/IonPHOSPHATE ION
Biological Unit 1 (3, 32)
No.NameCountTypeFull Name
11XC2Ligand/Ion6-({4-[(3,5-DIFLUOROPHENYL)SULFONYL]BENZYL}CARBAMOYL)-1-(5-O-PHOSPHONO-BETA-D-RIBOFURANOSYL)IMIDAZO[1,2-A]PYRIDIN-1-IUM
2EDO26Ligand/Ion1,2-ETHANEDIOL
3PO44Ligand/IonPHOSPHATE ION

(-) Sites  (16, 16)

Asymmetric Unit (16, 16)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREASP A:16 , TYR A:18 , TYR A:188 , HIS A:191 , PHE A:193 , ARG A:196 , ASP A:219 , SER A:241 , VAL A:242 , ALA A:244 , PRO A:273 , ARG A:311 , ASP A:313 , GLY A:353 , GLY A:383 , GLY A:384 , ARG A:392 , PO4 A:602 , PO4 A:609 , EDO A:610 , EDO A:612 , HOH A:735 , HOH A:760 , HOH A:838 , HOH A:910BINDING SITE FOR RESIDUE 1XC A 601
02AC2SOFTWARETYR A:18 , ARG A:196 , GLU A:246 , HIS A:247 , ARG A:311 , ASP A:313 , 1XC A:601 , PO4 A:609 , HOH A:714 , HOH A:830 , HOH A:879BINDING SITE FOR RESIDUE PO4 A 602
03AC3SOFTWAREHIS A:247 , THR A:251 , LYS A:400 , CYS A:401 , PHE A:414 , LYS A:415 , SER A:425 , HOH A:774BINDING SITE FOR RESIDUE EDO A 603
04AC4SOFTWARETYR A:23 , LYS A:24 , TYR A:26 , PRO A:27 , TYR A:142 , HIS A:264 , HOH A:775 , HOH A:887BINDING SITE FOR RESIDUE EDO A 604
05AC5SOFTWAREPHE A:123 , VAL A:124 , ASN A:479 , HOH A:894BINDING SITE FOR RESIDUE EDO A 605
06AC6SOFTWAREASP A:192 , GLY A:194 , TYR A:195 , ALA A:204 , GLY A:207 , ALA A:208 , THR A:220 , LEU A:387 , HOH A:780BINDING SITE FOR RESIDUE EDO A 606
07AC7SOFTWARESER A:180 , ASN A:337 , SER A:338 , GLU A:376 , HOH A:810 , HOH A:864BINDING SITE FOR RESIDUE EDO A 607
08AC8SOFTWAREPHE A:9 , ASN A:10 , LEU A:13 , ALA A:222 , HOH A:800BINDING SITE FOR RESIDUE EDO A 608
09AC9SOFTWAREARG A:196 , ARG A:392 , SER A:398 , LYS A:400 , 1XC A:601 , PO4 A:602 , EDO A:610 , HOH A:769 , HOH A:778 , HOH A:830 , HOH A:879BINDING SITE FOR RESIDUE PO4 A 609
10BC1SOFTWAREASP A:313 , ASP A:354 , LYS A:423 , 1XC A:601 , PO4 A:609 , HOH A:879BINDING SITE FOR RESIDUE EDO A 610
11BC2SOFTWARETYR A:54 , ASN A:164 , GLN A:168 , ASP A:357 , ILE A:358 , LEU A:386BINDING SITE FOR RESIDUE EDO A 611
12BC3SOFTWARETYR A:188 , 1XC A:601BINDING SITE FOR RESIDUE EDO A 612
13BC4SOFTWARELYS A:53 , TYR A:54 , GLU A:55 , GLU A:56 , GLU A:167 , LYS A:170BINDING SITE FOR RESIDUE EDO A 613
14BC5SOFTWAREASN A:67 , LYS A:71 , LYS A:229 , TYR A:230BINDING SITE FOR RESIDUE EDO A 614
15BC6SOFTWAREPRO A:120 , PHE A:123 , GLU A:475 , ASN A:479 , EDO A:616BINDING SITE FOR RESIDUE EDO A 615
16BC7SOFTWARELEU A:457 , HIS A:459 , EDO A:615BINDING SITE FOR RESIDUE EDO A 616

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4O16)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4O16)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4O16)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4O16)

(-) Exons   (0, 0)

(no "Exon" information available for 4O16)

(-) 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:470
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      
               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.......hhhhhhhhhhhhhh......hhhhhhhhhhhh..............hhhhhhhhhhhhhhhhhhhhhhhh....eeee....hhhhhhhh.....hhhhhh.......eeee....hhhhhhhhhhhhhhhhh..ee.....ee....eeeee....hhhhhhhhhhhhhhh..hhh.eeeeehhhhhhh.......eeeeeeeeee..eeee.......hhhhh......eeee.....eeee..hhhhhh.......eeeee..ee....hhhhhhhhh.hhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4o16 A   8 EFNILLATDSYKVTHYKQYPPNTSKVYSYFECREKKYEETVFYGLQYILNKYLKGKVVTKEKIQEAKDVYKEHFQDDVFNEKGWNYILEKYDGHLPIEIKAVPEGFVIPRGNVLFTVENTDPECYWLTNWIETILVQSWYPITVATNFREQKKILAKYLLETSGNLDGLEYKLHDFGYRGVSSQETAGIGASAHLVNFKGTDTVAGLALIKKYYGTKDPVPGYSVPAAEHSTITAWGKDHEKDAFEHIVTQFSSVPVSVVSDSYDIYNACEKIWGEDLRHLIVSRSTQAPLIIRPDSGNPLDTVLKVLEILGKKFPVTENSKGYKLLPPYLRVIQGDGVDINTLQEIVEGMKQKMWSIENIAFGSGGGLLQKLTRDLLNCSFKCSYVVTNGLGINVFKDPVADPNKRSKKGRLSLHRTPAGNFVTLEEGKGDLEEYGQDLLHTVFKNGKVTKSYSFDEIRKNAQLNIELE 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       387       397       407       417       427       437       447       457       467       477       487
                                                             42|                                                                                                                                                                                                                                                                                                                                                                                                                                                  
                                                              53                                                                                                                                                                                                                                                                                                                                                                                                                                                  

   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 4O16)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4O16)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4O16)

(-) Gene Ontology  (32, 32)

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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 4o15 4o17 4o18 4o19 4o1a 4o1b 4o1c 4o1d 4o28 4wq6 5kit 5u2m 5u2n 5upe 5upf

(-) Related Entries Specified in the PDB File

4o13 4o14 4o15 4o17 4o18 4o19 4o1a 4o1b 4o1c 4o1d 4o28