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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) - 09 Nov 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.71
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, 21)

Asymmetric/Biological Unit (3, 21)
No.NameCountTypeFull Name
1DGB2Ligand/Ion(2E)-N-{4-[1-(BENZENECARBONYL)PIPERIDIN-4-YL]BUTYL}-3-(PYRIDIN-3-YL)PROP-2-ENAMIDE
2EDO15Ligand/Ion1,2-ETHANEDIOL
3PO44Ligand/IonPHOSPHATE ION

(-) Sites  (21, 21)

Asymmetric Unit (21, 21)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREARG A:191 , PHE A:193 , ARG A:196 , ASP A:219 , VAL A:242 , ALA A:244 , PRO A:273 , SER A:275 , ILE A:309 , ARG A:311 , ILE A:351 , EDO A:608 , HOH A:779 , HOH A:913 , HOH A:1051 , HOH A:1117 , HOH A:1125 , TYR B:18BINDING SITE FOR RESIDUE DGB A 601
02AC2SOFTWAREARG A:40 , ARG A:392 , SER A:398 , LYS A:400 , EDO A:603 , HOH A:737 , HOH A:791 , HOH A:1194BINDING SITE FOR RESIDUE PO4 A 602
03AC3SOFTWAREARG A:40 , ARG A:392 , ASP A:393 , ASN A:396 , CYS A:397 , PO4 A:602BINDING SITE FOR RESIDUE EDO A 603
04AC4SOFTWAREASP A:313 , GLY A:353 , ASP A:354 , EDO A:606 , PO4 A:610 , HOH A:913 , HOH A:1193 , PO4 B:602 , HOH B:835BINDING SITE FOR RESIDUE EDO A 604
05AC5SOFTWAREHIS A:247 , SER A:248 , THR A:251 , HOH A:744 , LYS B:400 , CYS B:401 , PHE B:414 , SER B:425BINDING SITE FOR RESIDUE EDO A 605
06AC6SOFTWAREASP A:354 , GLY A:355 , GLY A:383 , GLY A:384 , EDO A:604 , HOH A:876BINDING SITE FOR RESIDUE EDO A 606
07AC7SOFTWAREGLY A:315 , PRO A:317 , ASP A:354 , HOH A:901 , HOH A:1038 , HOH A:1148BINDING SITE FOR RESIDUE EDO A 607
08AC8SOFTWARETYR A:188 , ARG A:191 , TYR A:240 , DGB A:601BINDING SITE FOR RESIDUE EDO A 608
09AC9SOFTWAREPHE A:123 , VAL A:124 , ARG A:434 , ASN A:479 , HOH A:842BINDING SITE FOR RESIDUE EDO A 609
10BC1SOFTWAREARG A:196 , GLU A:246 , HIS A:247 , ARG A:311 , ASP A:313 , EDO A:604 , HOH A:793 , TYR B:18 , HOH B:739 , HOH B:802BINDING SITE FOR RESIDUE PO4 A 610
11BC2SOFTWARETYR A:18 , TYR B:188 , ARG B:191 , PHE B:193 , ARG B:196 , ASP B:219 , ALA B:244 , PRO B:273 , SER B:275 , GLN B:305 , PRO B:307 , ILE B:309 , ARG B:311 , ILE B:351 , EDO B:605 , HOH B:763 , HOH B:1206BINDING SITE FOR RESIDUE DGB B 601
12BC3SOFTWAREARG A:196 , EDO A:604 , ARG B:392 , SER B:398 , LYS B:400 , EDO B:607 , HOH B:722 , HOH B:802BINDING SITE FOR RESIDUE PO4 B 602
13BC4SOFTWAREHOH A:1089 , GLY B:353 , GLY B:383 , GLY B:384 , HOH B:797 , HOH B:871 , HOH B:914 , HOH B:1036BINDING SITE FOR RESIDUE EDO B 603
14BC5SOFTWARELYS A:400 , CYS A:401 , PHE A:414 , HIS B:247 , SER B:248 , THR B:251 , HOH B:741BINDING SITE FOR RESIDUE EDO B 604
15BC6SOFTWARETYR B:188 , ARG B:191 , TYR B:240 , DGB B:601 , HOH B:815BINDING SITE FOR RESIDUE EDO B 605
16BC7SOFTWARETYR A:195 , HOH A:995 , PHE B:9 , ASN B:10 , LEU B:13 , HOH B:978 , HOH B:1127BINDING SITE FOR RESIDUE EDO B 606
17BC8SOFTWAREARG B:40 , ARG B:392 , ASP B:393 , ASN B:396 , CYS B:397 , SER B:398 , PO4 B:602BINDING SITE FOR RESIDUE EDO B 607
18BC9SOFTWARESER B:31 , LYS B:32 , ASN B:136 , ASP B:138 , PRO B:139 , HOH B:922BINDING SITE FOR RESIDUE EDO B 608
19CC1SOFTWAREPHE B:123 , VAL B:124 , ARG B:434 , ASN B:479 , HOH B:998BINDING SITE FOR RESIDUE EDO B 609
20CC2SOFTWARELYS B:169 , VAL B:213 , ASN B:214 , ARG B:477BINDING SITE FOR RESIDUE EDO B 610
21CC3SOFTWARETYR A:18 , HOH A:757 , HOH A:791 , ARG B:196 , GLU B:246 , HIS B:247 , ARG B:311 , ASP B:313 , HOH B:762 , HOH B:936BINDING SITE FOR RESIDUE PO4 B 611

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4O1D)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4O1D)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4O1D)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4O1D)

(-) Exons   (0, 0)

(no "Exon" information available for 4O1D)

(-) 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:471
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       
               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.eeeeehhhhhh........eeeeeeeeee..eeee.......hhhhh......eeee.....eeee..hhhhhh.......eeeee..ee....hhhhhhhhh.hhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4o1d A   8 EFNILLATDSYKVTHYKQYPPNTSKVYSYFECREKKKYEETVFYGLQYILNKYLKGKVVTKEKIQEAKDVYKEHFQDDVFNEKGWNYILEKYDGHLPIEIKAVPEGFVIPRGNVLFTVENTDPECYWLTNWIETILVQSWYPITVATNSREQKKILAKYLLETSGNLDGLEYKLRDFGYRGVSSQETAGIGASAHLVNFKGTDTVAGLALIKKYYGTKDPVPGYSVPAAEHSTITAWGKDHEKDAFEHIVTQFSSVPVSVVSDSYDIYNACEKIWGEDLRHLIVSRSTQAPLIIRPDSGNPLDTVLKVLEILGKKFPVTENSKGYKLLPPYLRVIQGDGVDINTLQEIVEGMKQKMWSIENIAFGSGGGLLQKLTRDLLNCSFKCSYVVTNGLGINVFKDPVADPNKRSKKGRLSLHRTPAGNFVTLEEGKGDLEEYGQDLLHTVFKNGKVTKSYSFDEIRKNAQLNIELE 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       386       396       406       416       426       436       446       456       466       476       486 
                                                              43|                                                                                                                                                                                                                                                                                                                                                                                                                                                  
                                                               53                                                                                                                                                                                                                                                                                                                                                                                                                                                  

Chain B from PDB  Type:PROTEIN  Length:469
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     
               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.....hhhhh........eeee....hhhhhhhhhhhhhhhhh..ee.....ee....eeeee....hhhhhhhhhhhhhhh..hhh.eeeeehhhhhh........eeeeeeeeee..eeee.......hhhhh......eeee.....eeee..hhhhhh.......eeeee..ee....hhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4o1d B   8 EFNILLATDSYKVTHYKQYPPNTSKVYSYFECREKKYEETVFYGLQYILNKYLKGKVVTKEKIQEAKDVYKEHFQDDVFNEKGWNYILEKYDGHLPIEIKAVPEGFVIPRGNVLFTVENTDPECYWLTNWIETILVQSWYPITVATNSREQKKILAKYLLETSGNLDGLEYKLRDFGYRGVSSQETAGIGASAHLVNFKGTDTVAGLALIKKYYGTKDPVPGYSVPAAEHSTITAWGKDHEKDAFEHIVTQFSSVPVSVVSDSYDIYNACEKIWGEDLRHLIVSRSTQAPLIIRPDSGNPLDTVLKVLEILGKKFPVTENSKGYKLLPPYLRVIQGDGVDINTLQEIVEGMKQKMWSIENIAFGSGGGLLQKLTRDLLNCSFKCSYVVTNGLGINVFKDPVADPNKRSKKGRLSLHRTPAGNFVTLEEGKGDLEEYGQDLLHTVFKNGKVTKSYSFDEIRKNAQLNIEL 486
                                    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         
                                                             42|                                                                                                                                                                                                                                                                                                                                                                                                                                                 
                                                              53                                                                                                                                                                                                                                                                                                                                                                                                                                                 

   Legend:   → Mismatch (orange background)
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    → 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 4O1D)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4O1D)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4O1D)

(-) 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 4o15 4o16 4o17 4o18 4o19 4o1a 4o1b 4o1c 4o28 4wq6 5kit 5u2m 5u2n 5upe 5upf

(-) Related Entries Specified in the PDB File

4o13 4o14 4o15 4o16 4o17 4o18 4o19 4o1a 4o1b 4o1c 4o28