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(-) Description

Title :  DISCOVERY OF POTENT AND EFFICACIOUS UREA-CONTAINING NICOTINAMIDE PHOSPHORIBOSYLTRANSFERASE (NAMPT) INHIBITORS WITH REDUCED CYP2C9 INHIBITION PROPERTIES
 
Authors :  J. Gunzner-Toste, G. Zhao, P. Bauer, T. Baumeister, A. J. Buckmelter, M. Caligiuri, K. H. Clodfelter, B. Fu, B. Han, Y. Ho, N. Kley, B. Liedere S. Mukadam, T. O'Brien, D. J. Reynolds, G. Sharma, N. Skelton, C. C. Smi W. Wang, Z. Wang, Y. Xiao, P. Yuen, M. Zak, L. Zhang, X. Zheng, K. W. Bair, P. S. Dragovich
Date :  15 Mar 13  (Deposition) - 29 May 13  (Release) - 05 Jun 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.20
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Transferase-Transferase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  J. Gunzner-Toste, G. Zhao, P. Bauer, T. Baumeister, A. J. Buckmelter, M. Caligiuri, K. H. Clodfelter, B. Fu, B. Han, Y. C. Ho, N. Kley, X. Liang B. M. Liederer, J. Lin, S. Mukadam, T. O'Brien, A. Oh, D. J. Reynolds, G. Sharma, N. Skelton, C. C. Smith, J. Sodhi, W. Wang, Z. Wang, Y. Xiao, P. W. Yuen, M. Zak, L. Zhang, X. Zheng, K. W. Bair, P. S. Dragovich
Discovery Of Potent And Efficacious Urea-Containing Nicotinamide Phosphoribosyltransferase (Nampt) Inhibitors With Reduced Cyp2C9 Inhibition Properties.
Bioorg. Med. Chem. Lett. V. 23 3531 2013
PubMed-ID: 23668988  |  Reference-DOI: 10.1016/J.BMCL.2013.04.040

(-) 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
11LJ2Ligand/Ion1-[(6-AMINOPYRIDIN-3-YL)METHYL]-3-[4-(PHENYLSULFONYL)PHENYL]UREA
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 , VAL A:242 , ALA A:244 , SER A:275 , ILE A:309 , ARG A:311 , ILE A:351 , ALA A:379 , EDO A:608 , HOH A:737 , HOH A:873 , HOH A:988 , ASP B:16 , TYR B:18BINDING SITE FOR RESIDUE 1LJ A 601
02AC2SOFTWAREGLU A:246 , HIS A:247 , ARG A:311 , ASP A:313 , HOH A:894 , TYR B:18BINDING SITE FOR RESIDUE PO4 A 602
03AC3SOFTWAREARG A:40 , ARG A:392 , SER A:398 , LYS A:400 , HOH A:724 , HOH A:791 , HOH A:818 , HOH A:820 , EDO B:606BINDING SITE FOR RESIDUE PO4 A 603
04AC4SOFTWAREPHE A:193 , GLY A:383 , GLY A:384 , HOH A:753 , HOH A:817 , HOH A:865 , ARG B:392BINDING SITE FOR RESIDUE EDO A 604
05AC5SOFTWAREPHE A:123 , VAL A:124 , ARG A:434 , ASN A:479BINDING SITE FOR RESIDUE EDO A 605
06AC6SOFTWARELYS A:400 , CYS A:401 , PHE A:414 , LYS A:415 , HOH A:830 , HIS B:247 , SER B:248 , THR B:251BINDING SITE FOR RESIDUE EDO A 606
07AC7SOFTWARELYS A:169 , GLU A:187 , VAL A:213 , ASN A:214 , ARG A:477 , HOH A:802BINDING SITE FOR RESIDUE EDO A 607
08AC8SOFTWARETYR A:188 , HIS A:191 , 1LJ A:601 , HOH A:731BINDING 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 , VAL B:242 , ALA B:244 , SER B:275 , ILE B:309 , ARG B:311 , ALA B:379 , HOH B:708 , HOH B:810 , HOH B:928BINDING SITE FOR RESIDUE 1LJ B 601
10BC1SOFTWAREARG B:40 , ARG B:392 , SER B:398 , LYS B:400 , HOH B:714 , HOH B:758 , HOH B:930BINDING SITE FOR RESIDUE PO4 B 602
11BC2SOFTWARETYR A:18 , ARG B:196 , GLU B:246 , HIS B:247 , ARG B:311 , ASP B:313 , HOH B:768BINDING SITE FOR RESIDUE PO4 B 603
12BC3SOFTWAREGLY B:353 , GLY B:383 , GLY B:384 , HOH B:815 , HOH B:891BINDING SITE FOR RESIDUE EDO B 604
13BC4SOFTWAREHIS A:247 , SER A:248 , THR A:251 , LYS B:400 , CYS B:401 , PHE B:414BINDING SITE FOR RESIDUE EDO B 605
14BC5SOFTWAREPO4 A:603 , HOH A:818 , ARG B:311 , ASP B:313 , GLY B:353 , ASP B:354 , HOH B:928BINDING SITE FOR RESIDUE EDO B 606
15BC6SOFTWAREHOH A:1012 , GLY B:315 , ASP B:354 , GLY B:355BINDING SITE FOR RESIDUE EDO B 607
16BC7SOFTWARETYR B:188 , TYR B:240 , VAL B:242 , HOH B:729 , HOH B:985BINDING SITE FOR RESIDUE EDO B 608

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Ala B:488 -Ala B:489

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4JNM)

(-) 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.....hhhhhhhhhhhhhhhh.....hhhhhhhhhhhhh....eeeee.....eee...eeeeeee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhh.eee.......hhhhhhhhhhhhh........hhhhhhhhhhh..............hhhhhhhhhhhhhhhhhhhhhhhh....eeee....hhhhhhhh.....hhhhh........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
                 4jnm A   8 EFNILLATDSYKVTHYKQYPPNTSKVYSYFECREKKKYEETVFYGLQYILNKYLKGKVVTKEKIQEAKDVYKEHFQDDVFNEKGWNYILEKYDGHLPIEIKAVPEGFVIPRGNVLFTVENTDPECYWLTNWIETILVQSWYPITVATNSREQKKILAKYLLETSGNLDGLEYKLHDFGYRGVSSQETAGIGASAHLVNFKGTDTVAGLALIKKYYGTKDPVPGYSVPAAEHSTITAWGKDHEKDAFEHIVTQFSSVPVSVVSDSYDIYNACEKIWGEDLRHLIVSRSTQAPLIIRPDSGNPLDTVLKVLEILGKKFPVTENSKGYKLLPPYLRVIQGDGVDINTLQEIVEGMKQKMWSIENIAFGSGGGLLQKLTRDLLNCSFKCSYVVTNGLGINVFKDPVADPNKRSKKGRLSLHRTPAGNFVTLEEGKGDLEEYGQDLLHTVFKNGKVTKSYSFDEIRKNAQLNIELE 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:473
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         
               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.hhhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4jnm B   8 EFNILLATDSYKVTHYKQYPPNTSKVYSYFECREKVKYEETVFYGLQYILNKYLKGKVVTKEKIQEAKDVYKEHFQDDVFNEKGWNYILEKYDGHLPIEIKAVPEGFVIPRGNVLFTVENTDPECYWLTNWIETILVQSWYPITVATNSREQKKILAKYLLETSGNLDGLEYKLHDFGYRGVSSQETAGIGASAHLVNFKGTDTVAGLALIKKYYGTKDPVPGYSVPAAEHSTITAWGKDHEKDAFEHIVTQFSSVPVSVVSDSYDIYNACEKIWGEDLRHLIVSRSTQAPLIIRPDSGNPLDTVLKVLEILGKKFPVTENSKGYKLLPPYLRVIQGDGVDINTLQEIVEGMKQKMWSIENIAFGSGGGLLQKLTRDLLNCSFKCSYVVTNGLGINVFKDPVADPNKRSKKGRLSLHRTPAGNFVTLEEGKGDLEEYGQDLLHTVFKNGKVTKSYSFDEIRKNAQLNIELEAA 489
                                    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)
  - → 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 4JNM)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (32, 32)

Asymmetric/Biological Unit(hide GO term definitions)

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  Cis Peptide Bonds
    Ala B:488 - Ala B:489   [ RasMol ]  
 

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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 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 4o28 4wq6 5kit 5u2m 5u2n 5upe 5upf

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 4JNM)