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(-) Description

Title :  STRUCTURE-BASED DISCOVERY OF NOVEL AMIDE-CONTAINING NICOTINAMIDE PHOSPHORIBOSYLTRANSFERASE (NAMPT) INHIBITORS
 
Authors :  X. Zheng, P. Bauer, T. Baumeister, A. J. Buckmelter, M. Caligiuri, K. H. Clodfelter, B. Han, Y. Ho, N. Kley, J. Lin, D. J. Reynolds, G. Sharm C. C. Smith, Z. Wang, P. S. Dragovich, J. Gunzner-Tosteb, B. M. Liedere T. O'Brien, A. Oh, L. Wang, W. Wang, Y. Xiao, M. Zak, G. Zhao, P. Yuen, K. W
Date :  27 Apr 13  (Deposition) - 08 May 13  (Release) - 10 Jul 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.60
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Transferase-Transferase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  X. Zheng, P. Bauer, T. Baumeister, A. J. Buckmelter, M. Caligiuri, K. H. Clodfelter, B. Han, Y. C. Ho, N. Kley, J. Lin, D. J. Reynolds, G. Sharma, C. C. Smith, Z. Wang, P. S. Dragovich, A. Oh, W. Wang, M. Zak, J. Gunzner-Toste, G. Zhao, P. W. Yuen, K. W. Bair
Structure-Based Identification Of Ureas As Novel Nicotinamide Phosphoribosyltransferase (Nampt) Inhibitors.
J. Med. Chem. V. 56 4921 2013
PubMed-ID: 23617784  |  Reference-DOI: 10.1021/JM400186H

(-) Compounds

Molecule 1 - NICOTINAMIDE PHOSPHORIBOSYLTRANSFERASE
    ChainsA, B
    EC Number2.4.2.12
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System Taxid562
    GeneNAMPT, PBEF, PBEF1
    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, 16)

Asymmetric/Biological Unit (3, 16)
No.NameCountTypeFull Name
11QS2Ligand/IonN-{4-[(3,5-DIFLUOROPHENYL)SULFONYL]BENZYL}IMIDAZO[1,2-A]PYRIDINE-6-CARBOXAMIDE
2EDO10Ligand/Ion1,2-ETHANEDIOL
3PO44Ligand/IonPHOSPHATE ION

(-) Sites  (16, 16)

Asymmetric Unit (16, 16)
No.NameEvidenceResiduesDescription
01AC1SOFTWARETYR A:188 , HIS A:191 , PHE A:193 , ARG A:196 , ASP A:219 , TYR A:240 , SER A:241 , VAL A:242 , ALA A:244 , PRO A:273 , ILE A:309 , ARG A:311 , ILE A:351 , HOH A:831 , HOH A:918 , HOH A:1001 , ASP B:16 , TYR B:18BINDING SITE FOR RESIDUE 1QS A 601
02AC2SOFTWAREARG A:196 , GLU A:246 , HIS A:247 , ARG A:311 , ASP A:313 , HOH A:727 , HOH A:784 , TYR B:18 , HOH B:730 , HOH B:733 , HOH B:790BINDING SITE FOR RESIDUE PO4 A 602
03AC3SOFTWAREARG A:392 , SER A:398 , LYS A:400 , EDO A:606 , HOH A:750 , HOH A:754 , HOH A:847 , ARG B:196BINDING SITE FOR RESIDUE PO4 A 603
04AC4SOFTWAREGLY A:315 , ASP A:354 , HOH A:880 , HOH A:1086 , HOH A:1224BINDING SITE FOR RESIDUE EDO A 604
05AC5SOFTWAREGLY A:353 , GLY A:383 , GLY A:384 , HOH A:770 , HOH A:966 , HOH A:1161BINDING SITE FOR RESIDUE EDO A 605
06AC6SOFTWAREARG A:40 , ARG A:392 , ASP A:393 , ASN A:396 , CYS A:397 , SER A:398 , PO4 A:603 , HOH A:1187BINDING SITE FOR RESIDUE EDO A 606
07AC7SOFTWARESER A:31 , ASN A:136 , THR A:137 , HOH A:1031 , HOH A:1175 , HOH A:1192BINDING SITE FOR RESIDUE EDO A 607
08AC8SOFTWARELYS A:400 , CYS A:401 , PHE A:414 , HOH A:745 , HIS B:247 , SER B:248 , THR B:251BINDING SITE FOR RESIDUE EDO A 608
09AC9SOFTWAREGLU A:187 , VAL A:213 , ASN A:214 , LYS A:216 , ARG A:477BINDING SITE FOR RESIDUE EDO A 609
10BC1SOFTWAREPHE A:123 , VAL A:124 , ARG A:434 , ASN A:479 , HOH A:862BINDING SITE FOR RESIDUE EDO A 610
11BC2SOFTWAREASP A:16 , TYR A:18 , HOH A:1233 , TYR B:188 , HIS B:191 , PHE B:193 , ARG B:196 , ASP B:219 , TYR B:240 , SER B:241 , VAL B:242 , ALA B:244 , SER B:275 , ILE B:309 , ARG B:311 , HOH B:780 , HOH B:995BINDING SITE FOR RESIDUE 1QS B 601
12BC3SOFTWAREARG A:196 , HOH A:784 , ARG B:392 , SER B:398 , LYS B:400 , EDO B:604 , HOH B:740 , HOH B:790 , HOH B:1093BINDING SITE FOR RESIDUE PO4 B 602
13BC4SOFTWARETYR A:18 , HOH A:739 , HOH A:745 , HOH A:750 , HOH A:847 , ARG B:196 , GLU B:246 , HIS B:247 , ARG B:311 , ASP B:313 , HOH B:717BINDING SITE FOR RESIDUE PO4 B 603
14BC5SOFTWAREARG B:40 , ARG B:392 , ASP B:393 , ASN B:396 , CYS B:397 , SER B:398 , PO4 B:602 , HOH B:871BINDING SITE FOR RESIDUE EDO B 604
15BC6SOFTWAREGLY B:353 , GLY B:383 , GLY B:384 , HOH B:832 , HOH B:838 , HOH B:1016BINDING SITE FOR RESIDUE EDO B 605
16BC7SOFTWAREHIS A:247 , SER A:248 , THR A:251 , LYS B:400 , CYS B:401 , PHE B:414 , HOH B:733BINDING SITE FOR RESIDUE EDO B 606

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4KFO)

(-) 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:472
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        
               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.......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
                 4kfo A   8 EFNILLATDSYKVTHYKQYPPNTSKVYSYFECREKKVKYEETVFYGLQYILNKYLKGKVVTKEKIQEAKDVYKEHFQDDVFNEKGWNYILEKYDGHLPIEIKAVPEGFVIPRGNVLFTVENTDPECYWLTNWIETILVQSWYPITVATNSREQKKILAKYLLETSGNLDGLEYKLHDFGYRGVSSQETAGIGASAHLVNFKGTDTVAGLALIKKYYGTKDPVPGYSVPAAEHSTITAWGKDHEKDAFEHIVTQFSSVPVSVVSDSYDIYNACEKIWGEDLRHLIVSRSTQAPLIIRPDSGNPLDTVLKVLEILGKKFPVTENSKGYKLLPPYLRVIQGDGVDINTLQEIVEGMKQKMWSIENIAFGSGGGLLQKLTRDLLNCSFKCSYVVTNGLGINVFKDPVADPNKRSKKGRLSLHRTPAGNFVTLEEGKGDLEEYGQDLLHTVFKNGKVTKSYSFDEIRKNAQLNIELE 487
                                    17        27        37     || 55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355       365       375       385       395       405       415       425       435       445       455       465       475       485  
                                                              43|                                                                                                                                                                                                                                                                                                                                                                                                                                                   
                                                               52                                                                                                                                                                                                                                                                                                                                                                                                                                                   

Chain B 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.....hhhhhhhhhhhhhhhh.....hhhhhhhhhhhhh....eeeee.....eee...eeeeeee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhh.eee.......hhhhhhhhhhhhh........hhhhhhhhhhh..............hhhhhhhhhhhhhhhhhhhhhhhh....eeee....hhhhhhhh.....hhhhhh.......eeee....hhhhhhhhhhhhhhhhh..ee.....ee....eeeee....hhhhhhhhhhhhhhh..hhh.eeeeehhhhhh........eeeeeeeeee..eeee.......hhhhh......eeee.....eeee..hhhhhh.......eeeee..ee....hhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4kfo B   8 EFNILLATDSYKVTHYKQYPPNTSKVYSYFECREKVKYEETVFYGLQYILNKYLKGKVVTKEKIQEAKDVYKEHFQDDVFNEKGWNYILEKYDGHLPIEIKAVPEGFVIPRGNVLFTVENTDPECYWLTNWIETILVQSWYPITVATNSREQKKILAKYLLETSGNLDGLEYKLHDFGYRGVSSQETAGIGASAHLVNFKGTDTVAGLALIKKYYGTKDPVPGYSVPAAEHSTITAWGKDHEKDAFEHIVTQFSSVPVSVVSDSYDIYNACEKIWGEDLRHLIVSRSTQAPLIIRPDSGNPLDTVLKVLEILGKKFPVTENSKGYKLLPPYLRVIQGDGVDINTLQEIVEGMKQKMWSIENIAFGSGGGLLQKLTRDLLNCSFKCSYVVTNGLGINVFKDPVADPNKRSKKGRLSLHRTPAGNFVTLEEGKGDLEEYGQDLLHTVFKNGKVTKSYSFDEIRKNAQLNIEL 486
                                    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
                                                             42|                                                                                                                                                                                                                                                                                                                                                                                                                                                  
                                                              52                                                                                                                                                                                                                                                                                                                                                                                                                                                  

   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 4KFO)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) 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 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 4o28 4wq6 5kit 5u2m 5u2n 5upe 5upf

(-) Related Entries Specified in the PDB File

4jr5 4kfn