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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 :  17 Dec 13  (Deposition) - 22 Oct 14  (Release) - 22 Oct 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
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
    Chains: A, B
    EC Number: 2.4.2.12
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: NAMPT, PBEF, PBEF1
    Mutation: YES
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: NAMPRTASE, 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, 19)

Asymmetric/Biological Unit (3, 19)
No.NameCountTypeFull Name
11QS2Ligand/IonN-{4-[(3,5-DIFLUOROPHENYL)SULFONYL]BENZYL}IMIDAZO[1,2-A]PYRIDINE-6-CARBOXAMIDE
2EDO13Ligand/Ion1,2-ETHANEDIOL
3PO44Ligand/IonPHOSPHATE ION

(-) Sites  (19, 19)

Asymmetric Unit (19, 19)
No.NameEvidenceResiduesDescription
01AC1SOFTWARETYR 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 , SER A:275 , ARG A:311 , ILE A:351 , HOH A:999 , HOH A:1017 , ASP B:16 , TYR B:18BINDING SITE FOR RESIDUE 1QS A 601
02AC2SOFTWAREARG A:196 , GLU A:246 , HIS A:247 , ARG A:311 , HOH A:757 , HOH A:1097 , TYR B:18 , HOH B:853BINDING SITE FOR RESIDUE PO4 A 602
03AC3SOFTWAREARG A:392 , SER A:398 , LYS A:400 , EDO A:605 , HOH A:765 , HOH A:771 , HOH A:783 , ARG B:196 , HOH B:1041BINDING SITE FOR RESIDUE PO4 A 603
04AC4SOFTWARELYS A:400 , CYS A:401 , PHE A:414 , HIS B:247 , SER B:248 , THR B:251 , HOH B:746BINDING SITE FOR RESIDUE EDO A 604
05AC5SOFTWAREARG A:40 , ARG A:392 , ASP A:393 , ASN A:396 , CYS A:397 , SER A:398 , PO4 A:603BINDING SITE FOR RESIDUE EDO A 605
06AC6SOFTWAREASP 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:1064BINDING SITE FOR RESIDUE EDO A 606
07AC7SOFTWAREPHE A:123 , VAL A:124 , ARG A:434 , ASN A:479 , HOH A:794BINDING SITE FOR RESIDUE EDO A 607
08AC8SOFTWAREGLU A:187 , VAL A:213 , ASN A:214 , PHE A:215 , LYS A:216 , ARG A:477BINDING SITE FOR RESIDUE EDO A 608
09AC9SOFTWAREASP A:16 , TYR A:18 , TYR B:188 , HIS B:191 , PHE B:193 , ARG B:196 , ASP B:219 , SER B:241 , VAL B:242 , ALA B:244 , PRO B:273 , SER B:275 , ARG B:311 , ILE B:351 , ALA B:379 , HOH B:739 , HOH B:886BINDING SITE FOR RESIDUE 1QS B 601
10BC1SOFTWAREARG A:196 , HOH A:1097 , ARG B:392 , SER B:398 , LYS B:400 , EDO B:607 , HOH B:731 , HOH B:774 , HOH B:853BINDING SITE FOR RESIDUE PO4 B 602
11BC2SOFTWARETYR A:18 , HOH A:783 , ARG B:196 , GLU B:246 , HIS B:247 , ARG B:311 , ASP B:313 , HOH B:730 , HOH B:1041BINDING SITE FOR RESIDUE PO4 B 603
12BC3SOFTWAREASP 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:958BINDING SITE FOR RESIDUE EDO B 604
13BC4SOFTWARESER A:199 , LYS A:389 , SER B:199BINDING SITE FOR RESIDUE EDO B 605
14BC5SOFTWAREHIS A:247 , SER A:248 , THR A:251 , LYS B:400 , CYS B:401 , PHE B:414 , LYS B:415 , SER B:425 , HOH B:776BINDING SITE FOR RESIDUE EDO B 606
15BC6SOFTWAREARG 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
16BC7SOFTWAREHOH A:834 , GLY B:315 , ASP B:354 , GLY B:355BINDING SITE FOR RESIDUE EDO B 608
17BC8SOFTWAREPRO A:27 , THR A:406 , HOH A:838 , TRP B:253 , HIS B:257 , HOH B:1045BINDING SITE FOR RESIDUE EDO B 609
18BC9SOFTWARESER A:241 , VAL A:242 , PRO A:243 , VAL A:272 , PHE B:91 , ASP B:93 , HOH B:991BINDING SITE FOR RESIDUE EDO B 610
19CC1SOFTWAREALA A:222 , ASN B:10 , LEU B:13BINDING SITE FOR RESIDUE EDO B 611

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4O28)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4O28)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4O28)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4O28)

(-) Exons   (0, 0)

(no "Exon" information available for 4O28)

(-) 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..............hhhhhhh....hhhhhhhhhhhhh....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
                 4o28 A   8 EFNILLATDSYKVTHYKQYPPNTSKVYSYFECREKYEETVFYGLQYILNKYLKGKVVTKEKIQEAKDVYKEHFQDDVFNEKGWNYILEKYDGHLPIEIKAVPEGFVIPRGNVLFTVENTDPECYWLTNWIETILVQSWYPITVATNFREQKKILAKYLLETSGNLDGLEYKLHDFGYRGVSSQETAGIGASAHLVNFKGTDTVAGLALIKKYYGTKDPVPGYSVPAAEHSTITAWGKDHEKDAFEHIVTQFSSVPVSVVSDSYDIYNACEKIWGEDLRHLIVSRSTQAPLIIRPDSGNPLDTVLKVLEILGKKFPVTENSKGYKLLPPYLRVIQGDGVDINTLQEIVEGMKQKMWSIENIAFGSGQKLTRDLLNCSFKCSYVVTNGLGINVFKDPVADPNKRSKKGRLSLHRTPAGNFVTLEEGKGDLEEYGQDLLHTVFKNGKVTKSYSFDEIRKNAQLNIELE 487
                                    17        27        37    ||  58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358       368       378    || 392       402       412       422       432       442       452       462       472       482     
                                                             42|                                                                                                                                                                                                                                                                                                                                      383|                                                                                                   
                                                              54                                                                                                                                                                                                                                                                                                                                       388                                                                                                   


Chain B from PDB  Type:PROTEIN  Length:464
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                
               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.hhhhhhhhhhhhhh.......hhhhhhhhhhh..............hhhhhhhhhhhhhhhhhhhhhhhh....eeee....hhhhhhhh.....hhhhhh.......eeee....hhhhhhhhhhhhhhhhh..ee.....ee....eeeee....hhhhhhhhhhhhhhh..hhh.eeeee........eeeeeeeeee..eeee.......hhhhh......eeee.....eeee..hhhhhh.......eeeee..ee....hhhhhhhhh....... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4o28 B   8 EFNILLATDSYKVTHYKQYPPNTSKVYSYFECREKKYEETVFYGLQYILNKYLKGKVVTKEKIQEAKDVYKEHFQDDVFNEKGWNYILEKYDGHLPIEIKAVPEGFVIPRGNVLFTVENTDPECYWLTNWIETILVQSWYPITVATNFREQKKILAKYLLETSGNLDGLEYKLHDFGYRGVSSQETAGIGASAHLVNFKGTDTVAGLALIKKYYGTKDPVPGYSVPAAEHSTITAWGKDHEKDAFEHIVTQFSSVPVSVVSDSYDIYNACEKIWGEDLRHLIVSRSTQAPLIIRPDSGNPLDTVLKVLEILGKKFPVTENSKGYKLLPPYLRVIQGDGVDINTLQEIVEGMKQKMWSIENIAFGSKLTRDLLNCSFKCSYVVTNGLGINVFKDPVADPNKRSKKGRLSLHRTPAGNFVTLEEGKGDLEEYGQDLLHTVFKNGKVTKSYSFDEIRKNAQLNIELE 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    || 393       403       413       423       433       443       453       463       473       483    
                                                             42|                                                                                                                                                                                                                                                                                                                                      382|                                                                                                  
                                                              53                                                                                                                                                                                                                                                                                                                                       389
   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 4O28)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4O28)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4O28)

(-) Gene Ontology  (32, 32)

Asymmetric/Biological Unit(hide GO term definitions)

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  4o28
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  2.4.2.12
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 Related Entries

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

UniProtKB/Swiss-Prot
        NAMPT_HUMAN | P43490: 2e5b 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 4o1d 4wq6 5kit 5u2m 5u2n 5upe 5upf

(-) Related Entries Specified in the PDB File

4o13 4o14 4o15 4o16 4o17 4o18 4o19 4o1a 4o1b 4o1c 4o1d