PDBsum entry 1ygc

Hydrolase

PDB id: 1ygc

Contents

Protein chains

254 a.a. *

53 a.a. *

Ligands

SO4 ×7

905

Metals

_CA ×2

Waters ×260

* Residue conservation analysis

PDB id:

1ygc

Name:

Hydrolase

Title:

Short factor viia with a small molecule inhibitor

Structure:

Coagulation factor vii. Chain: h. Fragment: heavy chain (residues 213-466). Synonym: serum prothrombin conversion accelerator, spca, proconvertin, eptacog alfa. Engineered: yes. Coagulation factor vii. Chain: l. Fragment: light chain, del 1-149 from full length (residues 150-212).

Source:

Homo sapiens. Human. Organism_taxid: 9606. Gene: f7. Expressed in: spodoptera frugiperda. Expression_system_taxid: 7108.

Biol. unit:

Dimer (from PQS)

Resolution:

2.00Å R-factor: 0.189 R-free: 0.205

Authors:

A.G.Olivero,C.Eigenbrot,R.Goldsmith,K.Robarge,D.R.Artis,J.Flygare, T.Rawson,C.Refino,S.Bunting,D.Kirchhofer

Key ref:

A.G.Olivero et al. (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. PubMed id: 15632123 DOI: 10.1074/jbc.M409068200

Date:

04-Jan-05 Release date: 18-Jan-05

Protein chain

P08709  (FA7_HUMAN) -  Coagulation factor VII from Homo sapiens

Seq: 466 a.a.

Struc: 254 a.a.

Protein chain

P08709  (FA7_HUMAN) -  Coagulation factor VII from Homo sapiens

Seq: 466 a.a.

Struc: 53 a.a.

Enzyme reactions

• Enzyme class: Chains H, L: E.C.3.4.21.21 - coagulation factor VIIa.
• Reaction: Hydrolyzes one Arg-|-Ile bond in factor X to form factor Xa.

DOI no: 10.1074/jbc.M409068200

J Biol Chem 280:9160-9169 (2005)

PubMed id: 15632123

A selective, slow binding inhibitor of factor VIIa binds to a nonstandard active site conformation and attenuates thrombus formation in vivo.

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, D.Kirchhofer.

ABSTRACT

The serine protease factor VIIa (FVIIa) in complex with its cellular cofactor tissue factor (TF) initiates the blood coagulation reactions. TF.FVIIa is also implicated in thrombosis-related disorders and constitutes an appealing therapeutic target for treatment of cardiovascular diseases. To this end, we generated the FVIIa active site inhibitor G17905, which displayed great potency toward TF.FVIIa (Ki = 0.35 +/- 0.11 nM). G17905 did not appreciably inhibit 12 of the 14 examined trypsin-like serine proteases, consistent with its TF.FVIIa-specific activity in clotting assays. The crystal structure of the FVIIa.G17905 complex provides insight into the molecular basis of the high selectivity. It shows that, compared with other serine proteases, FVIIa is uniquely equipped to accommodate conformational disturbances in the Gln217-Gly219 region caused by the ortho-hydroxy group of the inhibitor's aminobenzamidine moiety located in the S1 recognition pocket. Moreover, the structure revealed a novel, nonstandard conformation of FVIIa active site in the region of the oxyanion hole, a "flipped" Lys192-Gly193 peptide bond. Macromolecular substrate activation assays demonstrated that G17905 is a noncompetitive, slow-binding inhibitor. Nevertheless, G17905 effectively inhibited thrombus formation in a baboon arterio-venous shunt model, reducing platelet and fibrin deposition by approximately 70% at 0.4 mg/kg + 0.1 mg/kg/min infusion. Therefore, the in vitro potency of G17905, characterized by slow binding kinetics, correlated with efficacious antithrombotic activity in vivo.

Selected figure(s)

Figure 1.
FIG. 1. A, synthesis key intermediates. a, (i) LiCl, N,N-dimethylformamide 150 °C; (ii) BnCl, K[2]CO[3]. b, H[2], Pd/C, MeOH. c, t-butyldi-methylsilylchloride, imidazole. d (i) t-BuLi, B(OMe)[3], (ii) H[2]O[2]/AcOH. e, Cs[2]CO[3], EtI, N,N-dimethylformamide. f, t-BuLi, N,N-dimethylformamide. B, synthesis of G17905 [GenBank] . a, tosylmethylisocyanide, BF[3]OEt[2], MeOH/H[2]O. b, LiOH, tetrahydrofuran/H[2]O. c, CDI, m-nitrobenzene sulfonamide, DBU, tetrahydrofuran. d, H[2]/C/Pd. e, (i) EtOH, HCl; (ii) MeOH, NH[3]. f, reverse phase chiral chromatographic separation, S-WELK-O column, isopropyl alcohol, pH 5.5.

Figure 2.
FIG. 2. First generation sulfonamide- and acylsulfonamide-based FVIIa inhibitors.

The above figures are reprinted by permission from the ASBMB: J Biol Chem (2005, 280, 9160-9169) copyright 2005.

Figures were selected by an automated process.