PDBsum entry 1o5c

Blood clotting, hydrolase

PDB id: 1o5c

Contents

Protein chain

246 a.a. *

Ligands

LEU-LYS-PHE-GLN-CYS-GLY-GLN-LYS-THR

CR9

CIT ×2

Waters ×618

* Residue conservation analysis

PDB id:

1o5c

Name:

Blood clotting, hydrolase

Title:

Dissecting and designing inhibitor selectivity determinants at the s1 site using an artificial ala190 protease (ala190 upa)

Structure:

Urokinase-type plasminogen activator. Chain: a. Fragment: short chain. Synonym: upa, u-plasminogen activator. Engineered: yes. Urokinase-type plasminogen activator. Chain: b. Fragment: catalytic domain. Synonym: upa, u-plasminogen activator.

Source:

Homo sapiens. Human. Organism_taxid: 9606. Gene: plau. Expressed in: pichia pastoris. Expression_system_taxid: 4922.

Biol. unit:

Dimer (from PQS)

Resolution:

1.63Å R-factor: 0.191 R-free: 0.219

Authors:

B.A.Katz,C.Luong,J.D.Ho,J.R.Somoza,E.Gjerstad,J.Tang,S.R.Williams, E.Verner,R.L.Mackman,W.B.Young,P.A.Sprengeler,H.Chan,K.Mortara, J.W.Janc,M.E.Mcgrath

Key ref:

B.A.Katz et al. (2004). Dissecting and designing inhibitor selectivity determinants at the S1 site using an artificial Ala190 protease (Ala190 uPA). J Mol Biol, 344, 527-547. PubMed id: 15522303 DOI: 10.1016/j.jmb.2004.09.032

Date:

09-Sep-03 Release date: 21-Sep-04

Protein chain

P00749  (UROK_HUMAN) -  Urokinase-type plasminogen activator from Homo sapiens

Seq: 431 a.a.

Struc: 246 a.a.*

* PDB and UniProt seqs differ at 3 residue positions (black crosses)

Enzyme reactions

• Enzyme class: E.C.3.4.21.73 - u-plasminogen activator.
• Reaction: Specific cleavage of Arg-|-Val bond in plasminogen to form plasmin.

DOI no: 10.1016/j.jmb.2004.09.032

J Mol Biol 344:527-547 (2004)

PubMed id: 15522303

Dissecting and designing inhibitor selectivity determinants at the S1 site using an artificial Ala190 protease (Ala190 uPA).

B.A.Katz, C.Luong, J.D.Ho, J.R.Somoza, E.Gjerstad, J.Tang, S.R.Williams, E.Verner, R.L.Mackman, W.B.Young, P.A.Sprengeler, H.Chan, K.Mortara, J.W.Janc, M.E.McGrath.

ABSTRACT

A site-directed mutant of the serine protease urokinase-type plasminogen activator (uPA), was produced to assess the contribution of the Ser190 side-chain to the affinity and selectivity of lead uPA inhibitors in the absence of other differences present in comparisons of natural proteases. Crystallography and enzymology involving WT and Ala190 uPA were used to calculate free energy binding contributions of hydrogen bonds involving the Ser190 hydroxyl group (O(gamma)(Ser190)) responsible for the remarkable selectivity of 6-halo-5-amidinoindole and 6-halo-5-amidinobenzimidazole inhibitors toward uPA and against natural Ala190 protease anti-targets. Crystal structures of uPA complexes of novel, active site-directed arylguanidine and 2-aminobenzimidazole inhibitors of WT uPA, together with associated K(i) values for WT and Ala190 uPA, also indicate a significant role of Ser190 in the binding of these classes of uPA inhibitors. Structures and associated K(i) values for a lead inhibitor (CA-11) bound to uPA and to five other proteases, as well as for other leads bound to multiple proteases, help reveal the features responsible for the potency (K(i)=11nM) and selectivity of the remarkably small inhibitor, CA-11. The 6-fluoro-5-amidinobenzimidzole, CA-11, is more than 1000-fold selective against natural Ala190 protease anti-targets, and more than 100-fold selective against other Ser190 anti-targets.

Selected figure(s)

Figure 2.
Figure 2. Structure and associated (|F[o]| -|F[c]|), a[c] omit map for hepsin-CA-14, contoured at 2.5s.

Figure 9.
Figure 9. S1 site structure of the complex of WT uPA with the (a) 6-fluoro (CA-10) inhibitor and (b) the non-fluoro analog (CA-06). Short hydrogen bonds at the active site are cyan.

The above figures are reprinted by permission from Elsevier: J Mol Biol (2004, 344, 527-547) copyright 2004.

Figures were selected by an automated process.