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(-) Description

Title :  CREATING NOVEL F1 INHIBITORS THROUGH FRAGMENT BASED LEAD GENERATION AND STRUCTURE AIDED DRUG DESIGN
 
Authors :  J. Sandmark, L. Oster, O. Fjellstrom, S. Akkaya, H. G. Beisel, P. O. Erik K. Erixon, D. Gustafsson, U. Jurva, D. Kang, D. Karis, W. Knecht, V. Ner I. Nilsson, T. Olsson, A. Redzic, R. Roth, A. Tigerstrom
Date :  26 Feb 14  (Deposition) - 11 Feb 15  (Release) - 11 Feb 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.25
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (3x)
Keywords :  Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  O. Fjellstrom, S. Akkaya, H. Beisel, P. Eriksson, K. Erixon, D. Gustafsson, U. Jurva, D. Kang, D. Karis, W. Knecht, V. Nerme, I. Nilsson, T. Olsson, A. Redzic, R. Roth, J. Sandmark, A. Tigerstrom, L. Oster
Creating Novel Activated Factor Xi Inhibitors Through Fragment Based Lead Generation And Structure Aided Drug Design.
Plos One V. 10 13705 2015
PubMed-ID: 25629509  |  Reference-DOI: 10.1371/JOURNAL.PONE.0113705

(-) Compounds

Molecule 1 - COAGULATION FACTOR XI
    Chains: A
    EC Number: 3.4.21.27
    Engineered: YES
    Expression System: PICHIA PASTORIS
    Expression System Taxid: 4922
    Fragment: CATALYTIC DOMAIN, RESIDUES 388-625
    Mutation: YES
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: FXI, PLASMA THROMBOPLASTIN ANTECEDENT, PTA, COAGULATION FACTOR XIA LIGHT CHAIN

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit : A
Biological Unit 1 (3x): A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 9)

Asymmetric Unit (3, 9)
No.NameCountTypeFull Name
1GOL4Ligand/IonGLYCEROL
2J4X1Ligand/Ion6-CARBAMIMIDOYL-N-PHENYL-4-(PYRIMIDIN-2-YLAMINO)NAPHTHALENE-2-CARBOXAMIDE
3SO44Ligand/IonSULFATE ION
Biological Unit 1 (3, 27)
No.NameCountTypeFull Name
1GOL12Ligand/IonGLYCEROL
2J4X3Ligand/Ion6-CARBAMIMIDOYL-N-PHENYL-4-(PYRIMIDIN-2-YLAMINO)NAPHTHALENE-2-CARBOXAMIDE
3SO412Ligand/IonSULFATE ION

(-) Sites  (9, 9)

Asymmetric Unit (9, 9)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELEU A:39 , CYS A:40 , HIS A:57 , CYS A:58 , LYS A:192 , GLY A:193 , SER A:195 , J4X A:1493 , HOH A:2060 , HOH A:2325BINDING SITE FOR RESIDUE GOL A1489
2AC2SOFTWAREHIS A:34 , ARG A:37D , HIS A:38 , GLN A:74 , HOH A:2049 , HOH A:2116 , HOH A:2327 , HOH A:2328BINDING SITE FOR RESIDUE GOL A1490
3AC3SOFTWAREGLU A:26 , TRP A:27 , TRP A:137 , LYS A:157 , LYS A:202 , SO4 A:1494 , HOH A:2024 , HOH A:2025BINDING SITE FOR RESIDUE GOL A1491
4AC4SOFTWAREGLY A:25 , GLU A:26 , ARG A:119 , SO4 A:1494 , HOH A:2023BINDING SITE FOR RESIDUE GOL A1492
5AC5SOFTWAREHIS A:57 , SER A:81A , ASN A:113 , TYR A:114 , LEU A:146 , ASP A:189 , ALA A:190 , SER A:195 , TRP A:215 , GLY A:216 , GLU A:217 , GLY A:218 , GLY A:226 , GOL A:1489 , SO4 A:1495 , HOH A:2078 , HOH A:2264 , HOH A:2299 , HOH A:2330BINDING SITE FOR RESIDUE J4X A1493
6AC6SOFTWARELYS A:202 , TRP A:203 , GOL A:1491 , GOL A:1492 , HOH A:2024 , HOH A:2331BINDING SITE FOR RESIDUE SO4 A1494
7AC7SOFTWAREPHE A:83 , ASN A:113 , GLN A:118 , ARG A:147 , J4X A:1493 , HOH A:2111 , HOH A:2133 , HOH A:2192BINDING SITE FOR RESIDUE SO4 A1495
8AC8SOFTWARELYS A:127 , ARG A:130BINDING SITE FOR RESIDUE SO4 A1496
9AC9SOFTWARETHR A:20 , ALA A:21 , GLN A:48 , GLN A:86 , LYS A:107 , HOH A:2008 , HOH A:2239 , HOH A:2332 , HOH A:2333BINDING SITE FOR RESIDUE SO4 A1497

(-) SS Bonds  (4, 4)

Asymmetric Unit
No.Residues
1A:40 -A:58
2A:136 -A:201
3A:168 -A:182
4A:191 -A:219

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Ser A:37 -Pro A:37A

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4CRG)

(-) Sequences/Alignments

Asymmetric 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:234
                                                                                                                                                                                                                                                                           
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ....ee........eeeeee.....eeeeeeeeee..eeeehhhhhh...hhh.eeee.....hhhh......eeeeeeee.....hhhhh...eeeee................hhhhh...eeeee..............eeee..eehhhhhhhhh........eeee................eeeeee..eeeeeeeeee..........eeeee...hhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                4crg A   16 IVGGTASVRGEWPWQVTLHTTSPTQRHLCGGSIIGNQWILTAAHCFYGVESPKILRVYSGILNQAEIAEDTSFFGVQEIIIHDQYKMAESGYDIALLKLETTVNYADSQRPISLPSKGDRYTDCWVTGWGYRKLRDKIQNTLQKAKIPLVTNEECQKRYRGHKITHKMICAGYREGGKDACKGDSGGPLSCKHNEVWHLVGITSWGEGCAQRERPGVYTNVVEYVDWILEKTQA  244
                                    25        35  ||||  41      ||53      ||60        70        80 |      89        99       109       119|      130|      142      |153       163       173|      182  |    190      198B| |||| 210       220       230       240    
                                                37A|||         48|      59A||                    81A                                   119|      130|             149|                   173A        184A 188A       198A|| |||| ||                                   
                                                 37B||          51       59B|                                                           121       133              151                                                198B| |||| ||                                   
                                                  37C|                    59C                                                                                                                                           201 |||| ||                                   
                                                   37D                                                                                                                                                                   202A||| ||                                   
                                                                                                                                                                                                                          202B|| ||                                   
                                                                                                                                                                                                                           202C| ||                                   
                                                                                                                                                                                                                            202D ||                                   
                                                                                                                                                                                                                               204|                                   
                                                                                                                                                                                                                                209
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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 4CRG)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (19, 19)

Asymmetric Unit(hide GO term definitions)

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 Related Entries

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

UniProtKB/Swiss-Prot
        FA11_HUMAN | P03951: 1xx9 1xxd 1xxf 1zhm 1zhp 1zhr 1zjd 1zlr 1zmj 1zml 1zmn 1zom 1zpb 1zpc 1zpz 1zrk 1zsj 1zsk 1zsl 1ztj 1ztk 1ztl 2f83 2fda 2j8j 2j8l 3bg8 3sor 3sos 4cr5 4cr9 4cra 4crb 4crc 4crd 4cre 4crf 4d76 4d7f 4d7g 4na7 4na8 4ty6 4ty7 4wxi 4x6m 4x6n 4x6o 4x6p 4y8x 4y8y 4y8z 5e2o 5e2p 5eod 5eok 5exl 5exm 5exn 5i25 5q0d 5q0e 5q0f 5q0g 5q0h 5tks 5tkt 5tku

(-) Related Entries Specified in the PDB File

4cr5 CREATING NOVEL F1 INHIBITORS THROUGH FRAGMENT BASED LEAD GENERATION AND STRUCTURE AIDED DRUG DESIGN
4cr9 CREATING NOVEL F1 INHIBITORS THROUGH FRAGMENT BASED LEAD GENERATION AND STRUCTURE AIDED DRUG DESIGN
4cra CREATING NOVEL F1 INHIBITORS THROUGH FRAGMENT BASED LEAD GENERATION AND STRUCTURE AIDED DRUG DESIGN
4crb CREATING NOVEL F1 INHIBITORS THROUGH FRAGMENT BASED LEAD GENERATION AND STRUCTURE AIDED DRUG DESIGN
4crc CREATING NOVEL F1 INHIBITORS THROUGH FRAGMENT BASED LEAD GENERATION AND STRUCTURE AIDED DRUG DESIGN
4crd CREATING NOVEL F1 INHIBITORS THROUGH FRAGMENT BASED LEAD GENERATION AND STRUCTURE AIDED DRUG DESIGN
4cre CREATING NOVEL F1 INHIBITORS THROUGH FRAGMENT BASED LEAD GENERATION AND STRUCTURE AIDED DRUG DESIGN
4crf CREATING NOVEL F1 INHIBITORS THROUGH FRAGMENT BASED LEAD GENERATION AND STRUCTURE AIDED DRUG DESIGN