Crystal structure of hepatocyte growth factor activator complexed with kunitz domain inhibitor

Abstract

The present disclosure provides crystals of and structural coordinates of Hepatocyte growth factor activator with and without bound pseudo-substrate or inhibitor. In a specific embodiment, a crystal structure of activated HGFA complexed with a Kunitz domain inhibitor is provided. The crystals and crystal structures are useful, for example, in the design and synthesis of inhibitors of HGFA.

1 - 60 . (canceled) 
     
     
         61 . A computer-implemented method for causing a display of a graphical three-dimensional representation of the structure of at least a portion of a crystal of a HGFA or structural homolog thereof, wherein the method comprises:
 causing said display of said graphical three-dimensional representation by a computer system programmed with instructions for transforming structure coordinates into said graphical three-dimensional representation of said structure and for displaying said graphical three-dimensional representation,   wherein said graphical three-dimensional representation is generated by transforming said structure coordinates into said graphical three-dimensional representation of said structure,   wherein said structure coordinates comprise structure coordinates of the backbone atoms of the at least a portion of the crystal, and   wherein the at least a portion of the crystal comprises one or more of: a HGFA binding site or binding subsite, a fibronectin type II domain, an EGF-like domain, a fibronectin type I domain, a Kringle domain, and a trypsin-like serine protease domain.   
     
     
         62 . The method of  claim 61 , wherein the at least a portion of the crystal comprises a HGFA binding site, wherein the HGFA binding site is a binding site for KD1 or a binding site for HGF. 
     
     
         63 . The method of  claim 61 , wherein the at least a portion of the crystal comprises a HGFA binding subsite, wherein the HGFA binding subsite comprises a S1, S2, S3/4, S1′, S2′, or S3′ subsite. 
     
     
         64 . The method of  claim 61 , wherein the HGFA or structural homolog thereof is a HGFA. 
     
     
         65 . The method of  claim 61 , wherein the HGFA comprises SEQ ID NO:2. 
     
     
         66 . The method of  claim 61 , wherein the structure coordinates are defined in Table 7. 
     
     
         67 . The method of  claim 61 , wherein the structure coordinates comprise the structure coordinates of the backbone atoms of the amino acid residues corresponding to positions 489(95), 537(138), 559(160), 573(172), 576(175), 577(176), 581(180), 591(188), 592 (189), 593(190), 616(213), 617(214), 618(215), 619(216), 620(217), 621(219), 622(220), 626(223), 627(224), 628(225), 629(226), 630(227), and 631(228). 
     
     
         68 . The method of  claim 61 , wherein the structure coordinates comprise the structure coordinates of the backbone atoms of the amino acid residues, and wherein the structure coordinates of the backbone atoms have a root mean square deviation of less than about 0.70 Å from the structure coordinates of the backbone atoms of the amino acids as represented by the structure coordinates listed in Table 7. 
     
     
         69 . The method of  claim 61 , wherein the structure coordinates are determined by homology modeling. 
     
     
         70 . The method of  claim 61 , wherein the crystal has the space group symmetry P2 1 .