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(-) Description

Title :  FRAGMENT-BASED IDENTIFICATION OF AMIDES DERIVED FROM TRANS-2-(PYRIDIN-3-YL)CYCLOPROPANECARBOXYLIC ACID AS POTENT INHIBITORS OF HUMAN NICOTINAMIDE PHOSPHORIBOSYLTRANSFERASE (NAMPT)
 
Authors :  A. M. Giannetti, X. Zheng, N. Skelton, W. Wang, B. Bravo, Y. Feng, J. Gunz Toste, Y. Ho, R. Hua, C. Wang, Q. Zhao, B. M. Liederer, Y. Liu, T. O' Brie D. Sampath, Y. Shen, L. Wang, H. Wu, Y. Xiao, P. Yuen, M. Zak, G. Zhao, P. S. Dragovich
Date :  26 Jul 13  (Deposition) - 25 Sep 13  (Release) - 02 Oct 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.75
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Transferase, Transferase-Transferase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  X. Zheng, K. W. Bair, P. Bauer, T. Baumeister, K. K. Bowman, A. J. Buckmelter, M. Caligiuri, K. H. Clodfelter, Y. Feng, B. Han, Y. C. Ho, N. Kley, H. Li, X. Liang, B. M. Liederer, J. Lin, J. Ly, T. O'Brien, J. Oeh, A. Oh, D. J. Reynolds, D. Sampath, G. Sharma, N. Skelton, C. C. Smith, J. Tremayne, L. Wang, W. Wang, Z. Wang, H. Wu, J. Wu, Y. Xiao, G. Yang, P. W. Yuen, M. Zak, P. S. Dragovich
Identification Of Amides Derived From 1H-Pyrazolo[3, 4-B]Pyridine-5-Carboxylic Acid As Potent Inhibitors Of Human Nicotinamide Phosphoribosyltransferase (Nampt).
Bioorg. Med. Chem. Lett. V. 23 5488 2013
PubMed-ID: 24021463  |  Reference-DOI: 10.1016/J.BMCL.2013.08.074

(-) Compounds

Molecule 1 - NICOTINAMIDE PHOSPHORIBOSYLTRANSFERASE
    Chains: B, A
    EC Number: 2.4.2.12
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: NAMPT, PBEF, PBEF1
    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, 7)

Asymmetric/Biological Unit (3, 7)
No.NameCountTypeFull Name
11EB2Ligand/IonN-(4-NITROPHENYL)CYCLOPROPANECARBOXAMIDE
2EDO1Ligand/Ion1,2-ETHANEDIOL
3PO44Ligand/IonPHOSPHATE ION

(-) Sites  (7, 7)

Asymmetric Unit (7, 7)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG B:40 , ARG B:392 , SER B:398 , LYS B:400 , HOH B:712 , HOH B:860 , HOH B:902 , HOH B:1174 , HOH B:1175BINDING SITE FOR RESIDUE PO4 B 601
2AC2SOFTWAREGLY B:353 , GLY B:355 , GLY B:383 , GLY B:384 , GLY B:385 , HOH B:783 , HOH B:1108 , HOH B:1110 , HOH B:1177BINDING SITE FOR RESIDUE PO4 B 602
3AC3SOFTWARETYR A:18 , HIS B:191 , PHE B:193 , ARG B:196 , ASP B:219 , SER B:241 , VAL B:242 , ALA B:244 , ARG B:311 , HOH B:891BINDING SITE FOR RESIDUE 1EB B 603
4AC4SOFTWAREGLY A:197 , GLY A:384 , PO4 A:602 , ARG B:392 , HOH B:922BINDING SITE FOR RESIDUE EDO B 604
5AC5SOFTWAREARG A:40 , ARG A:392 , SER A:398 , LYS A:400 , HOH A:828 , HOH A:916 , HOH A:917 , HOH A:918 , HOH B:909BINDING SITE FOR RESIDUE PO4 A 601
6AC6SOFTWAREGLY A:353 , GLY A:355 , GLY A:383 , GLY A:384 , GLY A:385 , HOH A:810 , HOH A:849 , ARG B:392 , EDO B:604BINDING SITE FOR RESIDUE PO4 A 602
7AC7SOFTWAREHIS A:191 , PHE A:193 , ARG A:196 , ASP A:219 , SER A:241 , VAL A:242 , ALA A:244 , ARG A:311 , HOH A:814 , TYR B:18BINDING SITE FOR RESIDUE 1EB A 603

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4LVD)

(-) 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: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.....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
                 4lvd A   8 EFNILLATDSYKVTHYKQYPPNTSKVYSYFECREKKYEETVFYGLQYILNKYLKGKVVTKEKIQEAKDVYKEHFQDDVFNEKGWNYILEKYDGHLPIEIKAVPEGFVIPRGNVLFTVENTDPECYWLTNWIETILVQSWYPITVATNSREQKKILAKYLLETSGNLDGLEYKLHDFGYRGVSSQETAGIGASAHLVNFKGTDTVAGLALIKKYYGTKDPVPGYSVPAAEHSTITAWGKDHEKDAFEHIVTQFSSVPVSVVSDSYDIYNACEKIWGEDLRHLIVSRSTQAPLIIRPDSGNPLDTVLKVLEILGKKFPVTENSKGYKLLPPYLRVIQGDGVDINTLQEIVEGMKQKMWSIENIAFGSGGGLLQKLTRDLLNCSFKCSYVVTNGLGINVFKDPVADPNKRSKKGRLSLHRTPAGNFVTLEEGKGDLEEYGQDLLHTVFKNGKVTKSYSFDEIRKNAQLNIEL 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                                                                                                                                                                                                                                                                                                                                                                                                                                                 


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.....hhhhhhhhhhhhhhhh.....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...... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4lvd B   8 EFNILLATDSYKVTHYKQYPPNTSKVYSYFECREKKYEETVFYGLQYILNKYLKGKVVTKEKIQEAKDVYKEHFQDDVFNEKGWNYILEKYDGHLPIEIKAVPEGFVIPRGNVLFTVENTDPECYWLTNWIETILVQSWYPITVATNSREQKKILAKYLLETSGNLDGLEYKLHDFGYRGVSSQETAGIGASAHLVNFKGTDTVAGLALIKKYYGTKDPVPGYSVPAAEHSTITAWGKDHEKDAFEHIVTQFSSVPVSVVSDSYDIYNACEKIWGEDLRHLIVSRSTQAPLIIRPDSGNPLDTVLKVLEILGKKFPVTENSKGYKLLPPYLRVIQGDGVDINTLQEIVEGMKQKMWSIENIAFGSGGGLLQKLTRDLLNCSFKCSYVVTNGLGINVFKDPVADPNKRSKKGRLSLHRTPAGNFVTLEEGKGDLEEYGQDLLHTVFKNGKVTKSYSFDEIRKNAQLNIEL 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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  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 4LVD)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (32, 32)

Asymmetric/Biological Unit(hide GO term definitions)

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  4lvd
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  NAMPT_HUMAN | P43490
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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 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

4lv9 4lva 4lvb 4lvf 4lvg 4m6p 4m6q