PDBsum entry 1o5e

Serine protease, hydrolase

PDB id: 1o5e

Contents

Protein chains

110 a.a.

248 a.a. *

Ligands

132

Waters ×534

* Residue conservation analysis

PDB id:

1o5e

Name:

Serine protease, hydrolase

Title:

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

Structure:

Serine protease hepsin. Chain: l. Fragment: light chain. Synonym: transmembrane protease, serine 1. Engineered: yes. Mutation: yes. Serine protease hepsin. Chain: h. Fragment: heavy chain (catalytic domain).

Source:

Homo sapiens. Human. Organism_taxid: 9606. Gene: hpn or tmprss1. Expressed in: pichia pastoris. Expression_system_taxid: 4922. Expression_system_variant: km71. Expression_system_variant: km71

Biol. unit:

Dimer (from PQS)

Resolution:

1.75Å R-factor: 0.198 R-free: 0.227

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

P05981  (HEPS_HUMAN) -  Serine protease hepsin from Homo sapiens

Seq: 417 a.a.

Struc: 110 a.a.*

Protein chain

P05981  (HEPS_HUMAN) -  Serine protease hepsin from Homo sapiens

Seq: 417 a.a.

Struc: 248 a.a.

* PDB and UniProt seqs differ at 1 residue position (black cross)

Enzyme reactions

• Enzyme class: Chains L, H: E.C.3.4.21.106 - hepsin.

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.