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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 :  1.55
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
    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, 20)

Asymmetric/Biological Unit (3, 20)
No.NameCountTypeFull Name
120M2Ligand/IonN-(4-{[4-(PYRROLIDIN-1-YL)PIPERIDIN-1-YL]SULFONYL}BENZYL)-2H-PYRIDO[4,3-E][1,2,4]THIADIAZIN-3-AMINE 1,1-DIOXIDE
2EDO12Ligand/Ion1,2-ETHANEDIOL
3PO46Ligand/IonPHOSPHATE ION

(-) Sites  (20, 20)

Asymmetric Unit (20, 20)
No.NameEvidenceResiduesDescription
01AC1SOFTWARETYR A:188 , HIS A:191 , PHE A:193 , ASP A:219 , SER A:241 , VAL A:242 , ALA A:244 , ALA A:245 , SER A:275 , ILE A:309 , ARG A:311 , ILE A:351 , ALA A:379 , EDO A:607 , HOH A:712 , HOH A:854 , TYR B:18BINDING SITE FOR RESIDUE 20M A 601
02AC2SOFTWAREARG A:196 , GLU A:246 , HIS A:247 , ARG A:311 , HOH A:746 , HOH A:761 , HOH A:762 , TYR B:18 , HOH B:757 , HOH B:776BINDING SITE FOR RESIDUE PO4 A 602
03AC3SOFTWAREARG A:392 , SER A:398 , LYS A:400 , EDO A:606 , HOH A:719 , HOH A:731 , HOH A:736 , HOH A:747 , HOH A:753 , HOH A:1093 , ARG B:196 , PO4 B:603BINDING SITE FOR RESIDUE PO4 A 603
04AC4SOFTWAREPHE A:193 , GLY A:194 , ARG A:196 , GLY A:197 , GLY A:383 , GLY A:384 , EDO A:610 , HOH A:850 , HOH A:882 , HOH A:1072 , HOH A:1187 , ARG B:392BINDING SITE FOR RESIDUE PO4 A 604
05AC5SOFTWAREGLU A:187 , VAL A:213 , ASN A:214 , ARG A:477 , HOH A:1014BINDING SITE FOR RESIDUE EDO A 605
06AC6SOFTWAREARG A:40 , ARG A:392 , ASP A:393 , ASN A:396 , CYS A:397 , PO4 A:603 , HOH A:949 , HOH A:1093BINDING SITE FOR RESIDUE EDO A 606
07AC7SOFTWARELYS A:189 , ILE A:309 , ARG A:349 , VAL A:350 , ILE A:378 , ALA A:379 , 20M A:601 , HOH A:887BINDING SITE FOR RESIDUE EDO A 607
08AC8SOFTWAREGLY A:315 , PRO A:317 , ASP A:354 , GLY A:355 , HOH A:836 , HOH A:864 , HOH B:1038BINDING SITE FOR RESIDUE EDO A 608
09AC9SOFTWAREPHE A:123 , VAL A:124 , ARG A:434 , PHE A:440 , ASN A:479 , HOH A:837BINDING SITE FOR RESIDUE EDO A 609
10BC1SOFTWAREASP A:354 , GLY A:355 , GLY A:384 , PO4 A:604 , HOH A:734 , HOH A:745 , HOH A:850 , HOH A:882 , HOH B:964 , HOH B:1204BINDING SITE FOR RESIDUE EDO A 610
11BC2SOFTWARETYR 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 , ALA B:245 , ILE B:309 , ARG B:311 , ILE B:351 , ALA B:379 , HOH B:711 , HOH B:787 , HOH B:1011BINDING SITE FOR RESIDUE 20M B 601
12BC3SOFTWAREARG A:196 , HOH A:746 , ARG B:392 , SER B:398 , LYS B:400 , EDO B:605 , HOH B:720 , HOH B:739 , HOH B:747 , HOH B:776BINDING SITE FOR RESIDUE PO4 B 602
13BC4SOFTWARETYR A:18 , PO4 A:603 , HOH A:719 , HOH A:731 , HOH A:759 , ARG B:196 , GLU B:246 , HIS B:247 , ARG B:311 , HOH B:771 , HOH B:775BINDING SITE FOR RESIDUE PO4 B 603
14BC5SOFTWAREARG A:392 , PHE B:193 , GLY B:194 , ARG B:196 , GLY B:197 , GLY B:383 , GLY B:384 , EDO B:608 , HOH B:805 , HOH B:843 , HOH B:920 , HOH B:1000 , HOH B:1205BINDING SITE FOR RESIDUE PO4 B 604
15BC6SOFTWAREARG B:40 , ARG B:392 , ASP B:393 , ASN B:396 , CYS B:397 , SER B:398 , PO4 B:602 , EDO B:607BINDING SITE FOR RESIDUE EDO B 605
16BC7SOFTWAREHIS A:247 , SER A:248 , THR A:251 , HOH A:762 , LYS B:400 , CYS B:401 , PHE B:414 , LYS B:415 , SER B:425BINDING SITE FOR RESIDUE EDO B 606
17BC8SOFTWAREARG B:40 , ASP B:393 , ASN B:396 , EDO B:605 , HOH B:1038 , HOH B:1204BINDING SITE FOR RESIDUE EDO B 607
18BC9SOFTWAREASP B:354 , GLY B:355 , GLY B:384 , PO4 B:604 , HOH B:745 , HOH B:790 , HOH B:951 , HOH B:1000BINDING SITE FOR RESIDUE EDO B 608
19CC1SOFTWARELYS A:400 , CYS A:401 , PHE A:414 , HIS B:247 , SER B:248 , THR B:251 , HOH B:775BINDING SITE FOR RESIDUE EDO B 609
20CC2SOFTWARETYR A:195 , ALA A:222 , PHE B:9 , ASN B:10 , LEU B:13 , ALA B:14 , HOH B:901BINDING SITE FOR RESIDUE EDO B 610

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4LVA)

(-) 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.hhhhhhhhhhhhhh.......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
                 4lva 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:470
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      
               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
                 4lva B   8 EFNILLATDSYKVTHYKQYPPNTSKVYSYFECREKKYEETVFYGLQYILNKYLKGKVVTKEKIQEAKDVYKEHFQDDVFNEKGWNYILEKYDGHLPIEIKAVPEGFVIPRGNVLFTVENTDPECYWLTNWIETILVQSWYPITVATNSREQKKILAKYLLETSGNLDGLEYKLHDFGYRGVSSQETAGIGASAHLVNFKGTDTVAGLALIKKYYGTKDPVPGYSVPAAEHSTITAWGKDHEKDAFEHIVTQFSSVPVSVVSDSYDIYNACEKIWGEDLRHLIVSRSTQAPLIIRPDSGNPLDTVLKVLEILGKKFPVTENSKGYKLLPPYLRVIQGDGVDINTLQEIVEGMKQKMWSIENIAFGSGGGLLQKLTRDLLNCSFKCSYVVTNGLGINVFKDPVADPNKRSKKGRLSLHRTPAGNFVTLEEGKGDLEEYGQDLLHTVFKNGKVTKSYSFDEIRKNAQLNIELE 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       387       397       407       417       427       437       447       457       467       477       487
                                                             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 4LVA)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) 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 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

4lv9 4lvb 4lvd 4lvf 4lvg 4m6p 4m6q