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(-) Description

Title :  FACTOR XA IN COMPLEX WITH THE INHIBITOR 1-(4-METHOXYPHENYL)-6-(4-(1-(PYRROLIDIN-1-YLMETHYL)CYCLOPROPYL)PHENYL)-3-(TRIFLUOROMETHYL)-5,6-DIHYDRO-1H-PYRAZOLO[3,4-C]PYRIDIN-7(4H)-ONE
 
Authors :  R. S. Alexander
Date :  09 Apr 08  (Deposition) - 08 Jul 08  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.20
Chains :  Asym./Biol. Unit :  A,L
Keywords :  Glycoprotein, Hydrolase, Serine Protease, Plasma, Blood Coagulation Factor, Protein Inhibitor Complex, Calcium- Binding, Cleavage On Pair Of Basic Residues, Egf-Like Domain, Gamma-Carboxyglutamic Acid, Hydroxylation, Polymorphism, Zymogen, Blood Coagulation, Calcium, Protease (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  J. X. Qiao, D. L. Cheney, R. S. Alexander, A. M. Smallwood, S. R. King, K. He, A. R. Rendina, J. M. Luettgen, R. M. Knabb, R. R. Wexler, P. Y. Lam
Achieving Structural Diversity Using The Perpendicular Conformation Of Alpha-Substituted Phenylcyclopropanes To Mimic The Bioactive Conformation Of Ortho-Substituted Biphenyl P4 Moieties: Discovery Of Novel, Highly Potent Inhibitors Of Factor Xa.
Bioorg. Med. Chem. Lett. V. 18 4118 2008
PubMed-ID: 18550370  |  Reference-DOI: 10.1016/J.BMCL.2008.05.095
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - COAGULATION FACTOR X
    ChainsA
    EC Number3.4.21.6
    FragmentCOAGULATION FACTOR X, HEAVY CHAIN
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    Other DetailsPROTEOLYTIC CLEAVAGE PRODUCT
    SynonymSTUART FACTOR, STUART-PROWER FACTOR, FACTOR X LIGHT CHAIN, FACTOR X HEAVY CHAIN, ACTIVATED FACTOR XA HEAVY CHAIN
 
Molecule 2 - COAGULATION FACTOR X
    ChainsL
    EC Number3.4.21.6
    FragmentCOAGULATION FACTOR X, LIGHT CHAIN
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    Other DetailsPROTEOLYTIC CLEAVAGE PRODUCT
    SynonymSTUART FACTOR, STUART-PROWER FACTOR, FACTOR X LIGHT CHAIN, FACTOR X HEAVY CHAIN, ACTIVATED FACTOR XA HEAVY CHAIN

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit AL

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 2)

Asymmetric/Biological Unit (2, 2)
No.NameCountTypeFull Name
1CA1Ligand/IonCALCIUM ION
2LG01Ligand/Ion1-(4-METHOXYPHENYL)-6-(4-(1-(PYRROLIDIN-1-YLMETHYL)CYCLOPROPYL)PHENYL)-3-(TRIFLUOROMETHYL)-5,6-DIHYDRO-1H-PYRAZOLO[3,4-C]PYRIDIN-7(4H)-ONE

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:70 , ASN A:72 , GLN A:75 , GLU A:80BINDING SITE FOR RESIDUE CA A 301
2AC2SOFTWARELYS A:96 , GLU A:97 , THR A:98 , TYR A:99 , ARG A:143 , GLU A:146 , ASP A:189 , ALA A:190 , CYS A:191 , GLN A:192 , SER A:195 , TRP A:215 , GLY A:216 , GLY A:218 , CYS A:220 , GLY A:226BINDING SITE FOR RESIDUE LG0 A 298

(-) SS Bonds  (8, 8)

Asymmetric/Biological Unit
No.Residues
1A:22 -A:27
2A:42 -A:58
3A:122 -L:132
4A:168 -A:182
5A:191 -A:220
6L:89 -L:100
7L:96 -L:109
8L:111 -L:124

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3CS7)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (23, 23)

Asymmetric/Biological Unit (23, 23)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
01UniProtVAR_075213G262DFA10_HUMANUnclassified (FA10D)  ---AG43D
02UniProtVAR_065437G289RFA10_HUMANDisease (FA10D)121964946AG69R
03UniProtVAR_065438E304KFA10_HUMANDisease (FA10D)747292771AE84K
04UniProtVAR_065434E142KFA10_HUMANUnclassified (FA10D)61753266LE102K
05UniProtVAR_065439D322NFA10_HUMANDisease (FA10D)121964942AD102N
06UniProtVAR_065440R327WFA10_HUMANDisease (FA10D)770119164AR107W
07UniProtVAR_065435C149YFA10_HUMANDisease (FA10D)  ---LC109Y
08UniProtVAR_065436C151YFA10_HUMANDisease (FA10D)  ---LC111Y
09UniProtVAR_020176A152TFA10_HUMANPolymorphism3211772LA112T
10UniProtVAR_065441V338MFA10_HUMANDisease (FA10D)121964947AV118M
11UniProtVAR_065442E350KFA10_HUMANDisease (FA10D)372309538AE129K
12UniProtVAR_065443T358MFA10_HUMANDisease (FA10D)768222784AT135M
13UniProtVAR_065444G363SFA10_HUMANDisease (FA10D)  ---AG140S
14UniProtVAR_065445R366CFA10_HUMANDisease (FA10D)104894392AR143C
15UniProtVAR_065446S374PFA10_HUMANDisease (FA10D)121964941AS152P
16UniProtVAR_072751V382AFA10_HUMANDisease (FA10D)  ---AV160A
17UniProtVAR_065447P383SFA10_HUMANDisease (FA10D)121964940AP161S
18UniProtVAR_065448C390FFA10_HUMANDisease (FA10D)199778916AC168F
19UniProtVAR_065449C404RFA10_HUMANDisease (FA10D)  ---AC182R
20UniProtVAR_065450G406SFA10_HUMANDisease (FA10D)376163818AG184S
21UniProtVAR_065451G420RFA10_HUMANDisease (FA10D)750759634AG196R
22UniProtVAR_072752G421DFA10_HUMANDisease (FA10D)758726161AG197D
23UniProtVAR_065452K448NFA10_HUMANDisease (FA10D)  ---AK224N

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

(-) PROSITE Motifs  (4, 4)

Asymmetric/Biological Unit (4, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1EGF_2PS01186 EGF-like domain signature 2.FA10_HUMAN110-121
149-164
  1-
L:109-124
2TRYPSIN_DOMPS50240 Serine proteases, trypsin domain profile.FA10_HUMAN235-467  1A:16-243
3TRYPSIN_HISPS00134 Serine proteases, trypsin family, histidine active site.FA10_HUMAN272-277  1A:53-58
4TRYPSIN_SERPS00135 Serine proteases, trypsin family, serine active site.FA10_HUMAN413-424  1A:189-200

(-) Exons   (4, 5)

Asymmetric/Biological Unit (4, 5)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1bENST000003755591bENSE00001885902chr13:113777132-113777239108FA10_HUMAN1-24240--
1.2ENST000003755592ENSE00001757906chr13:113783766-113783926161FA10_HUMAN24-77540--
1.4ENST000003755594ENSE00001666002chr13:113792771-11379279525FA10_HUMAN78-8690--
1.5ENST000003755595ENSE00001614193chr13:113793671-113793784114FA10_HUMAN86-124390--
1.6cENST000003755596cENSE00000862532chr13:113795233-113795364132FA10_HUMAN124-168451-
L:87-128
-
42
1.7aENST000003755597aENSE00001710199chr13:113798165-113798409245FA10_HUMAN168-249822A:16-30
L:128-138
15
11
1.8eENST000003755598eENSE00000862534chr13:113801693-113801810118FA10_HUMAN250-289401A:31-69
-
40
-
1.9cENST000003755599cENSE00001616173chr13:113803230-113803843614FA10_HUMAN289-4882001A:69-244 (gaps)
-
182
-

(-) 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:234
 aligned with FA10_HUMAN | P00742 from UniProtKB/Swiss-Prot  Length:488

    Alignment length:234
                                   244       254       264       274       284       294       304       314       324       334       344       354       364       374       384       394       404       414       424       434       444       454       464    
          FA10_HUMAN    235 IVGGQECKDGECPWQALLINEENEGFCGGTILSEFYILTAAHCLYQAKRFKVRVGDRNTEQEEGGEAVHEVEVVIKHNRFTKETYDFDIAVLRLKTPITFRMNVAPACLPERDWAESTLMTQKTGIVSGFGRTHEKGRQSTRLKMLEVPYVDRNSCKLSSSFIITQNMFCAGYDTKQEDACQGDSGGPHVTRFKDTYFVTGIVSWGEGCARKGKYGIYTKVTAFLKWIDRSMKT  468
               SCOP domains d3cs7a_ A: automated matches                                                                                                                                                                                                               SCOP domains
               CATH domains 3cs7A01     3cs7A02 A:28-120,A:233-244 Trypsin-like serine proteases                                      3cs7A01 A:16-27,A:121-232 Trypsin-like serine proteases                                                             3cs7A02      CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ....ee........eeeee.....eeeeeee....eeeehhhhhhh....eeee............eee.eeeeee.............eeeee................hhhhhhhhh....eeeeee..............eeeeeeeehhhhhhhhh.......eeee................eeeeee..eeeeeeeeee..........eeeee...hhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------D--------------------------R--------------K-----------------N----W----------M-----------K-------M----S--C-------P-------AS------F-------------R-S-------------RD--------------------------N-------------------- SAPs(SNPs)
                PROSITE (1) TRYPSIN_DOM  PDB: A:16-243 UniProt: 235-467                                                                                                                                                                                              - PROSITE (1)
                PROSITE (2) -------------------------------------TRYPSI---------------------------------------------------------------------------------------------------------------------------------------TRYPSIN_SER -------------------------------------------- PROSITE (2)
           Transcript 1 (1) ---------------Exon 1.8e  PDB: A:31-69 UniProt: 250-289----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript 1 (1)
           Transcript 1 (2) Exon 1.7a      ---------------------------------------Exon 1.9c  PDB: A:69-244 (gaps) UniProt: 289-488 [INCOMPLETE]                                                                                                                        Transcript 1 (2)
                3cs7 A   16 IVGGQECKDGECPWQALLINEENEGFCGGTILSEFYILTAAHCLYQAKRFKVRVGDRNTEQEEGGEAVHEVEVVIKHNRFTKETYDFDIAVLRLKTPITFRMNVAPACLPERDWAESTLMTQKTGIVSGFGRTHEKGRQSTRLKMLEVPYVDRNSCKLSSSFIITQNMFCAGYDTKQEDACQGDSGGPHVTRFKDTYFVTGIVSWGEGCARKGKYGIYTKVTAFLKWIDRSMKT  244
                                    25        35        45        55      | 64        74        84        94       104       114       124|     131B       141     ||152       162       172       182   ||  190       200       210       221  |    230       240    
                                                                        61A                                                            124A    131A|             147|                                 185A|                              218|   |                     
                                                                                                                                                131B              149                                  185B                               220   |                     
                                                                                                                                                                                                                                             223A                     

Chain L from PDB  Type:PROTEIN  Length:52
 aligned with FA10_HUMAN | P00742 from UniProtKB/Swiss-Prot  Length:488

    Alignment length:52
                                   136       146       156       166       176  
          FA10_HUMAN    127 KLCSLDNGDCDQFCHEEQNSVVCSCARGYTLADNGKACIPTGPYPCGKQTLE  178
               SCOP domains d3cs7l_ L: automated matches                         SCOP domains
               CATH domains 3cs7L00 L:87-138 Laminin                             CATH domains
               Pfam domains ---------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhh..eeee....eeee....eee......eee............ Sec.struct. author
                 SAPs(SNPs) ---------------K------Y-YT-------------------------- SAPs(SNPs)
                PROSITE (1) ----------------------EGF_2           -------------- PROSITE (1)
                PROSITE (2) ---------------------------------------------------- PROSITE (2)
           Transcript 1 (1) Exon 1.6c  PDB: L:87-128 UniProt: 124-168 ---------- Transcript 1 (1)
           Transcript 1 (2) -----------------------------------------Exon 1.7a   Transcript 1 (2)
                3cs7 L   87 KLCSLDNGDCDQFCHEEQNSVVCSCARGYTLADNGKACIPTGPYPCGKQTLE  138
                                    96       106       116       126       136  

   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  (2, 2)

Asymmetric/Biological Unit

(-) CATH Domains  (2, 3)

Asymmetric/Biological Unit
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3CS7)

(-) Gene Ontology  (22, 22)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,L   (FA10_HUMAN | P00742)
molecular function
    GO:0005509    calcium ion binding    Interacting selectively and non-covalently with calcium ions (Ca2+).
    GO:0016787    hydrolase activity    Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
    GO:0008233    peptidase activity    Catalysis of the hydrolysis of a peptide bond. A peptide bond is a covalent bond formed when the carbon atom from the carboxyl group of one amino acid shares electrons with the nitrogen atom from the amino group of a second amino acid.
    GO:0005543    phospholipid binding    Interacting selectively and non-covalently with phospholipids, a class of lipids containing phosphoric acid as a mono- or diester.
    GO:0005515    protein binding    Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
    GO:0004252    serine-type endopeptidase activity    Catalysis of the hydrolysis of internal, alpha-peptide bonds in a polypeptide chain by a catalytic mechanism that involves a catalytic triad consisting of a serine nucleophile that is activated by a proton relay involving an acidic residue (e.g. aspartate or glutamate) and a basic residue (usually histidine).
    GO:0008236    serine-type peptidase activity    Catalysis of the hydrolysis of peptide bonds in a polypeptide chain by a catalytic mechanism that involves a catalytic triad consisting of a serine nucleophile that is activated by a proton relay involving an acidic residue (e.g. aspartate or glutamate) and a basic residue (usually histidine).
biological process
    GO:0006888    ER to Golgi vesicle-mediated transport    The directed movement of substances from the endoplasmic reticulum (ER) to the Golgi, mediated by COP II vesicles. Small COP II coated vesicles form from the ER and then fuse directly with the cis-Golgi. Larger structures are transported along microtubules to the cis-Golgi.
    GO:0007596    blood coagulation    The sequential process in which the multiple coagulation factors of the blood interact, ultimately resulting in the formation of an insoluble fibrin clot; it may be divided into three stages: stage 1, the formation of intrinsic and extrinsic prothrombin converting principle; stage 2, the formation of thrombin; stage 3, the formation of stable fibrin polymers.
    GO:0007598    blood coagulation, extrinsic pathway    A protein activation cascade that contributes to blood coagulation and consists of the self-limited process linking exposure and activation of tissue factor to the activation of clotting factor X.
    GO:0007597    blood coagulation, intrinsic pathway    A protein activation cascade that contributes to blood coagulation and consists of the interactions among high molecular weight kininogen, prekallikrein, and factor XII that lead to the activation of clotting factor X.
    GO:0007599    hemostasis    The stopping of bleeding (loss of body fluid) or the arrest of the circulation to an organ or part.
    GO:0017187    peptidyl-glutamic acid carboxylation    The gamma-carboxylation of peptidyl-glutamic acid; catalyzed by the vitamin K dependent gamma-glutamyl carboxylase.
    GO:0030335    positive regulation of cell migration    Any process that activates or increases the frequency, rate or extent of cell migration.
    GO:0051897    positive regulation of protein kinase B signaling    Any process that activates or increases the frequency, rate or extent of protein kinase B signaling, a series of reactions mediated by the intracellular serine/threonine kinase protein kinase B.
    GO:0006508    proteolysis    The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds.
    GO:0006465    signal peptide processing    The proteolytic removal of a signal peptide from a protein during or after transport to a specific location in the cell.
cellular component
    GO:0005796    Golgi lumen    The volume enclosed by the membranes of any cisterna or subcompartment of the Golgi apparatus, including the cis- and trans-Golgi networks.
    GO:0005788    endoplasmic reticulum lumen    The volume enclosed by the membranes of the endoplasmic reticulum.
    GO:0005576    extracellular region    The space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane. This term covers the host cell environment outside an intracellular parasite.
    GO:0031233    intrinsic component of external side of plasma membrane    The component of a plasma membrane consisting of gene products and protein complexes that penetrate the external side of the plasma membrane only, either directly or via some covalently attached hydrophobic anchor.
    GO:0005886    plasma membrane    The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.

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 Related Entries

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

UniProtKB/Swiss-Prot
        FA10_HUMAN | P007421c5m 1ezq 1f0r 1f0s 1fax 1fjs 1fxy 1g2l 1g2m 1hcg 1ioe 1iqe 1iqf 1iqg 1iqh 1iqi 1iqj 1iqk 1iql 1iqm 1iqn 1ksn 1lpg 1lpk 1lpz 1lqd 1mq5 1mq6 1msx 1nfu 1nfw 1nfx 1nfy 1nl8 1p0s 1v3x 1wu1 1xka 1xkb 1z6e 2bmg 2boh 2bok 2bq6 2bq7 2bqw 2cji 2d1j 2ei6 2ei7 2ei8 2fzz 2g00 2gd4 2h9e 2j2u 2j34 2j38 2j4i 2j94 2j95 2jkh 2p16 2p3f 2p3t 2p3u 2p93 2p94 2p95 2phb 2pr3 2q1j 2ra0 2uwl 2uwo 2uwp 2vh0 2vh6 2vvc 2vvu 2vvv 2vwl 2vwm 2vwn 2vwo 2w26 2w3i 2w3k 2wyg 2wyj 2xbv 2xbw 2xbx 2xby 2xc0 2xc4 2xc5 2y5f 2y5g 2y5h 2y7x 2y7z 2y80 2y81 2y82 3cen 3ens 3ffg 3hpt 3iit 3k9x 3kl6 3kqb 3kqc 3kqd 3kqe 3liw 3m36 3m37 3q3k 3sw2 3tk5 3tk6 4a7i 4bti 4btt 4btu 4y6d 4y71 4y76 4y79 4y7a 4y7b 4zh8 4zha 5jqy 5jtc 5jz8 5jzu 5k0h

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 3CS7)