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(-) Description

Title :  RAPID DEVELOPMENT OF TWO FACTOR IXA INHIBITORS FROM HIT TO LEAD
 
Authors :  A. Hruza, P. Reichert
Date :  25 Mar 15  (Deposition) - 20 May 15  (Release) - 20 May 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.41
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Serine Proteinase, Blood Coagulation, Coagulation Factor, Hydrolase- Hydrolase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  D. L. Parker, S. Walsh, B. Li, E. Kim, A. Sharipour, C. Smith, Y. H. Chen, R. Berger, B. Harper, T. Zhang, M. Park, M. Shu, J. Wu, J. Xu, S. Dewnani, E. C. Sherer, A. Hruza, P. Reichert, W. Geissler, L. Sonatore, K. Ellsworth, J. Balkovec, W. Greenlee, H. B. Wood
Rapid Development Of Two Factor Ixa Inhibitors From Hit To Lead.
Bioorg. Med. Chem. Lett. V. 25 2321 2015
PubMed-ID: 25937013  |  Reference-DOI: 10.1016/J.BMCL.2015.04.025

(-) Compounds

Molecule 1 - COAGULATION FACTOR IX
    Chains: A
    EC Number: 3.4.21.22
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Fragment: PEPTIDASE S1 DOMAIN (UNP RESIDUE 227-461)
    Gene: F9
    Mutation: YES
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: CHRISTMAS FACTOR,PLASMA THROMBOPLASTIN COMPONENT,PTC
 
Molecule 2 - COAGULATION FACTOR IX
    Chains: B
    EC Number: 3.4.21.22
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Fragment: EGF-LIKE 2 DOMAIN (UNP RESIDUES 131-191)
    Gene: F9
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: CHRISTMAS FACTOR,PLASMA THROMBOPLASTIN COMPONENT,PTC

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (4, 4)
No.NameCountTypeFull Name
14K61Ligand/IonN-[2-(5,6-DIMETHYL-1H-BENZIMIDAZOL-2-YL)ETHYL]-4-(4H-1,2,4-TRIAZOL-4-YL)BENZAMIDE
2CL1Ligand/IonCHLORIDE ION
3NA1Ligand/IonSODIUM ION
4NHE1Ligand/Ion2-[N-CYCLOHEXYLAMINO]ETHANE SULFONIC ACID

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:87 , TYR A:99 , PHE A:174 , SER A:190 , CYS A:191 , GLN A:192 , SER A:195 , ILE A:213 , TRP A:215 , GLY A:216 , GLU A:217 , CYS A:220 , HOH A:480 , HOH A:495 , HOH A:499binding site for residue 4K6 A 301
2AC2SOFTWAREGLU A:70 , ASN A:72 , GLU A:75 , GLU A:77 , GLU A:80 , HOH A:411binding site for residue NA A 302
3AC3SOFTWAREASP A:21 , LYS A:132 , PHE A:145 , ALA A:152 , LEU A:153 , VAL A:154 , HOH A:426 , HOH A:465 , HOH A:483 , HOH A:607binding site for residue NHE A 303
4AC4SOFTWAREARG A:83 , HOH A:516 , HOH A:542 , LEU B:117binding site for residue CL B 201

(-) SS Bonds  (7, 7)

Asymmetric/Biological Unit
No.Residues
1A:42 -A:58
2A:122 -B:132
3A:168 -A:182
4A:191 -A:220
5B:88 -B:99
6B:95 -B:109
7B:111 -B:124

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4YZU)

(-) 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:235
                                                                                                                                                                                                                                                                            
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....ee........eeeee......eeeeeee..eeeehhhhh......eeee............eeeeeeeeee...............eeeee................hhhhhhhhhhh.eeeeee..............eeeeee..hhhhhhhh........eeee................eeeeee..eeeeeeeeee..........eeeee...hhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                4yzu A   16 VVGGEDAKPGQFPWQVVLNGKVDAFCGGSIVNEKWIVTAAHCVETGVKITVVAGEHNIEETEHTEQKRNVIRIIPHHNYNAAINKYNHDIALLELDEPLVLNSYVTPICIADKEYTNIFLKFGSGYVSGWGRVFHKGASALVLQYLRVPLVDRATCLRSTKFTIYNNMFCAGFHEGGRDSCQGDSGGPHVTEVEGTSFLTGIISWGEECAMKGKYGIYTKVSRYVNWIKEKTKLT  245
                                    25        35||      46        56    |   65        75        85        95||     103       113       123      |131       141   ||  152       162       172       182  |    190       200       210      |221|      230       240     
                                               36|                    60A                                 95A|                               129A|             145|                                  184A 188A                          217|  |                        
                                                38                                                         95B                                129B              147                                                                      219  |                        
                                                                                                                                                                                                                                           221A                        


Chain B from PDB  Type:PROTEIN  Length:57
                                                                                          
               SCOP domains --------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------- Pfam domains
         Sec.struct. author ......hhhhhh..eeee.....eeee....eee......eee.............. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------- Transcript
                4yzu B   84 MDVTCNIKNGRCEQFCKNSADNKVVCSCTEGYRLAENQKSCEPAVPFPCGRVSVSQT  140
                                    93       103       113       123       133
   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 4YZU)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (22, 22)

Asymmetric/Biological Unit(hide GO term definitions)

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  3.4.21.22
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 Related Entries

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

UniProtKB/Swiss-Prot
        FA9_HUMAN | P00740: 1cfh 1cfi 1edm 1ixa 1mgx 1nl0 1rfn 2wph 2wpi 2wpj 2wpk 2wpl 2wpm 3kcg 3lc3 3lc5 4wm0 4wma 4wmb 4wmi 4wmk 4wn2 4wnh 4z0k 4zae 5egm 5f84 5f85 5f86 5jb8 5jb9 5jba 5jbb 5jbc 5tno 5tnt

(-) Related Entries Specified in the PDB File

4z0k