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PDBsum entry 1w2k
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protein ligands metals Protein-protein interface(s) links
Hydrolase PDB id
1w2k

 

 

 

 

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Contents
Protein chains
251 a.a. *
142 a.a. *
188 a.a. *
Ligands
380
CAC
FUC
BGC
Metals
_CA ×9
Waters ×372
* Residue conservation analysis
PDB id:
1w2k
Name: Hydrolase
Title: Tf7a_4380 complex
Structure: Blood coagulation factor viia. Chain: h. Fragment: factor vii heavy chain, residues 213-466. Synonym: serum prothrombin conversion accelerator, spca, proconvertin, eptacog alfa, novoseven. Engineered: yes. Blood coagulation factor viia. Chain: l. Fragment: factor vii heavy chain, residues 61-202.
Source: Homo sapiens. Human. Organism_taxid: 9606. Expressed in: mesocricetus auratus. Expression_system_taxid: 10036. Expression_system_cell_line: kidney cells (bhk). Expressed in: escherichia coli. Expression_system_taxid: 562
Resolution:
3.00Å     R-factor:   0.197     R-free:   0.257
Authors: D.W.Banner,A.D'Arcy,K.Groebke-Zbinden,J.Ackermann,D.Kirchhofer,Y.- H.Ji,T.B.Tschopp,S.Wallbaum,L.Weber
Key ref: K.Groebke Zbinden et al. (2005). Design of selective phenylglycine amide tissue factor/factor VIIa inhibitors. Bioorg Med Chem Lett, 15, 817-822. PubMed id: 15664864 DOI: 10.1016/j.bmcl.2004.10.092
Date:
06-Jul-04     Release date:   20-Jun-05    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P08709  (FA7_HUMAN) -  Coagulation factor VII from Homo sapiens
Seq:
Struc: 		466 a.a.
251 a.a.
Protein chain
Pfam   ArchSchema ?
P08709  (FA7_HUMAN) -  Coagulation factor VII from Homo sapiens
Seq:
Struc: 		466 a.a.
142 a.a.*
Protein chain
Pfam   ArchSchema ?
P13726  (TF_HUMAN) -  Tissue factor from Homo sapiens
Seq:
Struc: 		295 a.a.
188 a.a.
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 9 residue positions (black crosses)

 Enzyme reactions 
   Enzyme class: Chains H, L: E.C.3.4.21.21  - coagulation factor VIIa.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: Hydrolyzes one Arg-|-Ile bond in factor X to form factor Xa.

 

 
DOI no: 10.1016/j.bmcl.2004.10.092 Bioorg Med Chem Lett 15:817-822 (2005)
PubMed id: 15664864  
 
 
Design of selective phenylglycine amide tissue factor/factor VIIa inhibitors.
K.Groebke Zbinden, D.W.Banner, J.Ackermann, A.D'Arcy, D.Kirchhofer, Y.H.Ji, T.B.Tschopp, S.Wallbaum, L.Weber.
 
  ABSTRACT  
 
Proof of concept experiments have shown that tissue factor/factor VIIa inhibitors have antithrombotic activity without enhancing bleeding propensity. Starting from lead compounds generated by a biased combinatorial approach, phenylglycine amide tissue factor/factor VIIa inhibitors with low nanomolar affinity and good selectivity against other serine proteases of the coagulation cascade were designed, using the guidance of X-ray structural analysis and molecular modelling.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
17006949 A.Poleksic, J.F.Danzer, B.A.Palmer, B.D.Olafson, and D.A.Debe (2006).
SPINFAST: using structure alignment profiles to enhance the accuracy and assess the reliability of protein side-chain modeling.
  Proteins, 65, 953-958.  
16757484 S.P.Bajaj, A.E.Schmidt, S.Agah, M.S.Bajaj, and K.Padmanabhan (2006).
High resolution structures of p-aminobenzamidine- and benzamidine-VIIa/soluble tissue factor: unpredicted conformation of the 192-193 peptide bond and mapping of Ca2+, Mg2+, Na+, and Zn2+ sites in factor VIIa.
  J Biol Chem, 281, 24873-24888.
PDB codes: 2a2q 2aer 2fir
15632123 A.G.Olivero, C.Eigenbrot, R.Goldsmith, K.Robarge, D.R.Artis, J.Flygare, T.Rawson, D.P.Sutherlin, S.Kadkhodayan, M.Beresini, L.O.Elliott, G.G.DeGuzman, D.W.Banner, M.Ultsch, U.Marzec, S.R.Hanson, C.Refino, S.Bunting, and D.Kirchhofer (2005).
A selective, slow binding inhibitor of factor VIIa binds to a nonstandard active site conformation and attenuates thrombus formation in vivo.
  J Biol Chem, 280, 9160-9169.
PDB code: 1ygc
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB codes are shown on the right.

 

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