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(-) Description

Title :  POTENT, REVERSIBLE METAP2 INHIBITORS VIA FRAGMENT BASED DRUG DISCOVERY
 
Authors :  D. R. Dougan, J. D. Lawson
Date :  19 Apr 16  (Deposition) - 25 May 16  (Release) - 15 Jun 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.60
Chains :  Asym./Biol. Unit :  A
Keywords :  Hydrolase, Peptidase, Metal Ion Binding, Proteolysis, Hydrolase- Hydrolase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  C. Mcbride, Z. Cheruvallath, M. Komandla, M. Tang, P. Farrell, J. D. Lawson, D. Vanderpool, Y. Wu, D. R. Dougan, A. Plonowski, C. Holub C. Larson
Discovery Of Potent, Reversible Metap2 Inhibitors Via Fragment Based Drug Discovery And Structure Based Drug Design-Part 2.
Bioorg. Med. Chem. Lett. V. 26 2779 2016
PubMed-ID: 27136719  |  Reference-DOI: 10.1016/J.BMCL.2016.04.072

(-) Compounds

Molecule 1 - METHIONINE AMINOPEPTIDASE 2
    Chains: A
    EC Number: 3.4.11.18
    Engineered: YES
    Expression System: SPODOPTERA FRUGIPERDA
    Expression System Strain: SF9
    Expression System Taxid: 7108
    Fragment: UNP RESIDUES 87-455
    Gene: METAP2, MNPEP, P67EIF2
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: METAP 2,INITIATION FACTOR 2-ASSOCIATED 67 KDA GLYCOPROTEIN, P67EIF2,PEPTIDASE M

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 5)

Asymmetric/Biological Unit (4, 5)
No.NameCountTypeFull Name
16KP1Ligand/Ion7-FLUORO-4-(5-METHYL-3H-IMIDAZO[4,5-B]PYRIDIN-6-YL)-2,4-DIHYDROPYRAZOLO[4,3-B]INDOLE
2DMS1Ligand/IonDIMETHYL SULFOXIDE
3EDO1Ligand/Ion1,2-ETHANEDIOL
4MN2Ligand/IonMANGANESE (II) ION

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:251 , ASP A:262 , GLU A:459 , MN A:502 , HOH A:609 , HOH A:642binding site for residue MN A 501
2AC2SOFTWAREASP A:262 , HIS A:331 , GLU A:364 , GLU A:459 , MN A:501 , 6KP A:505 , HOH A:642binding site for residue MN A 502
3AC3SOFTWARETYR A:383 , ARG A:417 , LEU A:432 , LYS A:433 , HOH A:658 , HOH A:742binding site for residue DMS A 503
4AC4SOFTWAREGLY A:190 , THR A:192 , GLU A:195 , GLN A:243 , HOH A:620 , HOH A:733binding site for residue EDO A 504
5AC5SOFTWAREPRO A:220 , HIS A:231 , ASP A:262 , HIS A:331 , HIS A:339 , GLU A:364 , HIS A:382 , ALA A:414 , TYR A:444 , MN A:502 , HOH A:609 , HOH A:642binding site for residue 6KP A 505

(-) SS Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1A:228 -A:448

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Asp A:114 -Pro A:115

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 5JFR)

(-) 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    
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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:366
                                                                                                                                                                                                                                                                                                                                                                                                              
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .........hhhhhh........eee...........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhh.....eeeeeeeeeee..eee.................eeeeeeeee..eeeeeeeee..hhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhh..eeee..eeee.ee.....eeee.........ee............eeeeeeeee......ee.....eeee..........hhhhhhhhhhhhhhh....eehhhhhhh....hhhhhhhhhhh..eeee..ee......eeeeeeeeee....eee....... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 5jfr A 110 KVQTDPPSVPICDLYPNGVFPKGQECEYPPTQDGRTAAWRTTSEEKKALDQASEEIWNDFREAAEAHRQVRKYVMSWIKPGMTMIEICEKLEDCSRKLIKENGLNAGLAFPTGCSLNNCAAHYTPNAGDTTVLQYDDICKIDFGTHISGRIIDCAFTVTFNPKYDTLLKAVKDATNTGIKCAGIDVRLCDVGEAIQEVMESYEVEIDGKTYQVKPIRNLNGHSIGQYRIHAGKTVPIVKGTRMEEGEVYAIETFGSTGKGVVHDDMECSHYMKNFDVGHVPIRLPRTKHLLNVINENFGTLAFCRRWLDRLGESKYLMALKNLCDLGIVDPYPPLCDIKGSYTAQFEHTILLRPTCKEVVSRGDDY 478
                                   119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339       349|      362       372       382       392       402       412       422       432       442       452       462       472      
                                                                                                                                                                                                                                                                         349|                                                                                                                             
                                                                                                                                                                                                                                                                          353
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  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 5JFR)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (15, 15)

Asymmetric/Biological Unit(hide GO term definitions)

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  MAP2_HUMAN | P50579
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  3.4.11.18
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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        MAP2_HUMAN | P50579: 1b59 1b6a 1bn5 1boa 1kq0 1kq9 1qzy 1r58 1r5g 1r5h 1yw7 1yw8 1yw9 2adu 2ea2 2ea4 2ga2 2oaz 5cls 5d6e 5d6f 5jhu 5ji6

(-) Related Entries Specified in the PDB File

5jhu 5ji6