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(-) Description

Title :  CRYSTAL STRUCTURE OF HUMAN NAMPT WITH A-1293201
 
Authors :  K. L. Longenecker, D. Raich, A. V. Korepanova
Date :  30 Nov 16  (Deposition) - 28 Jun 17  (Release) - 28 Jun 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.89
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Nampt Inhibitor, Transferase-Transferase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. L. Wilsbacher, M. Cheng, D. Cheng, S. A. J. Trammell, Y. Shi, J. Guo, S. L. Koeniger, P. J. Kovar, Y. He, S. Selvaraju, H. R. Heyman, B. K. Sorensen, R. F. Clark, T. M. Hansen, K. L. Longenecker, D. Raich, A. V. Korepanova, S. Cepa, D. L. Towne, V. C. Abraham, H. Tang, P. L. Richardson, S. M. Mcloughlin, I. Badagnani, M. L. Curtin, M. R. Michaelides, D. Maag, F. G. Buchanan, G. G. Chiang, W. Gao, S. H. Rosenberg, C. Brenner, C. Tse
Discovery And Characterization Of Novel Non-Substrate And Substrate Nampt Inhibitors.
Mol. Cancer Ther. 2017
PubMed-ID: 28468779  |  Reference-DOI: 10.1158/1535-7163.MCT-16-0819

(-) Compounds

Molecule 1 - NICOTINAMIDE PHOSPHORIBOSYLTRANSFERASE
    Chains: A, B
    EC Number: 2.4.2.12
    Engineered: YES
    Expression System: MAMMALIA
    Expression System Cell Line: HEK 293-6E
    Expression System Taxid: 40674
    Gene: NAMPT, PBEF, PBEF1
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: 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  (2, 8)

Asymmetric/Biological Unit (2, 8)
No.NameCountTypeFull Name
17T72Ligand/IonN-[4-({[(3S)-OXOLAN-3-YL]METHYL}CARBAMOYL)PHENYL]-1,3-DIHYDRO-2H-ISOINDOLE-2-CARBOXAMIDE
2SO46Ligand/IonSULFATE ION

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETYR A:188 , HIS A:191 , PHE A:193 , ARG A:196 , ASP A:219 , VAL A:242 , ALA A:244 , PRO A:273 , SER A:275 , ILE A:309 , ARG A:311 , ILE A:351 , ALA A:379 , SO4 A:902 , HOH A:1085 , HOH A:1129 , HOH A:1177 , TYR B:18binding site for residue 7T7 A 901
2AC2SOFTWAREARG A:196 , GLU A:246 , HIS A:247 , ARG A:311 , ASP A:313 , 7T7 A:901 , HOH A:1005 , HOH A:1156 , TYR B:18 , HOH B:643binding site for residue SO4 A 902
3AC3SOFTWAREARG A:392 , SER A:398 , LYS A:400 , HOH A:1027 , HOH A:1181binding site for residue SO4 A 903
4AC4SOFTWAREARG A:392 , HOH A:1064 , HOH A:1176 , GLY B:197 , GLY B:383 , GLY B:384 , HOH B:615binding site for residue SO4 A 904
5AC5SOFTWARETYR A:18 , TYR B:188 , HIS B:191 , PHE B:193 , ARG B:196 , ASP B:219 , VAL B:242 , ALA B:244 , PRO B:273 , SER B:275 , ILE B:309 , ARG B:311 , ILE B:351 , ALA B:379 , HOH B:716 , HOH B:735binding site for residue 7T7 B 501
6AC6SOFTWAREARG A:196 , ARG B:40 , ARG B:392 , SER B:398 , LYS B:400binding site for residue SO4 B 502
7AC7SOFTWAREGLY A:197 , GLY A:383 , GLY A:384 , ARG B:392 , ASP B:393 , HOH B:608 , HOH B:662binding site for residue SO4 B 503
8AC8SOFTWARETYR A:18 , HOH A:1027 , HOH A:1065 , ARG B:196 , GLU B:246 , HIS B:247 , ARG B:311 , ASP B:313 , HOH B:687 , HOH B:787binding site for residue SO4 B 504

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5U2M)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 5U2M)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5U2M)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5U2M)

(-) Exons   (0, 0)

(no "Exon" information available for 5U2M)

(-) 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: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.....eeeee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhh.eee.......hhhhhhhhhhhhh........hhhhhhhhhhh..............hhhhhhhhhhhhhhhhhhhhhhhh....eeee....hhhhhhhh.....hhhhhh.......eeee....hhhhhhhhhhhhhhhhh..ee.....ee....eeeee....hhhhhhhhhhhhhhh..hhh.eeeeehhhhhh........eeeeeeeeee..eeee.......hhhhh......eeee.....eeee..hhhhh........eeeee..ee....hhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5u2m A   9 FNILLATDSYKVTHYKQYPPNTSKVYSYFECREYEETVFYGLQYILNKYLKGKVVTKEKIQEAKDVYKEHFQDDVFNEKGWNYILEKYDGHLPIEIKAVPEGFVIPRGNVLFTVENTDPECYWLTNWIETILVQSWYPITVATNSREQKKILAKYLLETSGNLDGLEYKLHDFGYRGVSSQETAGIGASAHLVNFKGTDTVAGLALIKKYYGTKDPVPGYSVPAAEHSTITAWGKDHEKDAFEHIVTQFSSVPVSVVSDSYDIYNACEKIWGEDLRHLIVSRSTQAPLIIRPDSGNPLDTVLKVLEILGKKFPVTENSKGYKLLPPYLRVIQGDGVDINTLQEIVEGMKQKMWSIENIAFGSGGGLLQKLTRDLLNCSFKCSYVVTNGLGINVFKDPVADPNKRSKKGRLSLHRTPAGNFVTLEEGKGDLEEYGQDLLHTVFKNGKVTKSYSFDEIRKNAQLNI 484
                                    18        28        38  ||    60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420       430       440       450       460       470       480    
                                                           41|                                                                                                                                                                                                                                                                                                                                                                                                                                              
                                                            54                                                                                                                                                                                                                                                                                                                                                                                                                                              


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.....hhhhhhhhhhhhhhhh.....hhhhhhhhhhhhh....eeeee.....eee...eeeeeee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhh.eee.hhhhh.hhhhhhhhhhhhh........hhhhhhhhhhh..............hhhhhhhhhhhhhhhhhhhhhhhh....eeee....hhhhhhhh.....hhhhhh.......eeee....hhhhhhhhhhhhhhhhh..ee.....ee....eeeee....hhhhhhhhhhhhhhh..hhh.eeeeehhhhhh........eeeeeeeeee..eeee.......hhhhh......eeee.....eeee..hhhhhhhhh....eeeee..ee....hhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5u2m B   9 FNILLATDSYKVTHYKQYPPNTSKVYSYFECREYEETVFYGLQYILNKYLKGKVVTKEKIQEAKDVYKEHFQDDVFNEKGWNYILEKYDGHLPIEIKAVPEGFVIPRGNVLFTVENTDPECYWLTNWIETILVQSWYPITVATNSREQKKILAKYLLETSGNLDGLEYKLHDFGYRGVSSQETAGIGASAHLVNFKGTDTVAGLALIKKYYGTKDPVPGYSVPAAEHSTITAWGKDHEKDAFEHIVTQFSSVPVSVVSDSYDIYNACEKIWGEDLRHLIVSRSTQAPLIIRPDSGNPLDTVLKVLEILGKKFPVTENSKGYKLLPPYLRVIQGDGVDINTLQEIVEGMKQKMWSIENIAFGSGGGLLQKLTRDLLNCSFKCSYVVTNGLGINVFKDPVADPNKRSKKGRLSLHRTPAGNFVTLEEGKGDLEEYGQDLLHTVFKNGKVTKSYSFDEIRKNAQLNI 484
                                    18        28        38  ||    60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420       430       440       450       460       470       480    
                                                           41|                                                                                                                                                                                                                                                                                                                                                                                                                                              
                                                            54
   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 5U2M)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5U2M)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5U2M)

(-) Gene Ontology  (32, 32)

Asymmetric/Biological Unit(hide GO term definitions)

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  5u2m
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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 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 5u2n 5upe 5upf

(-) Related Entries Specified in the PDB File

5u2n