PDBsum entry 1ghw

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Hydrolase/hydrolase inhibitor PDB id
Protein chains
36 a.a. *
250 a.a. *
11 a.a. *
Waters ×1155
* Residue conservation analysis
PDB id:
Name: Hydrolase/hydrolase inhibitor
Title: A novel serine protease inhibition motif involving a multi-c short hydrogen bonding network at the active site
Structure: Thrombin. Chain: l. Fragment: light chain, residues 328-363. Synonym: coagulation factor ii. Thrombin. Chain: h. Fragment: heavy chain, residues 364-620. Synonym: coagulation factor ii. Acetyl hirudin.
Source: Homo sapiens. Human. Organism_taxid: 9606. Synthetic: yes. Hirudo medicinalis. Organism_taxid: 6421
Biol. unit: Tetramer (from PQS)
1.75Å     R-factor:   0.196     R-free:   0.234
Authors: B.A.Katz,K.Elrod,C.Luong,M.Rice,R.L.Mackman,P.A.Sprengeler,J J.Hatayte,J.Janc,J.Link,J.Litvak,R.Rai,K.Rice,S.Sideris,E.V W.Young
Key ref:
B.A.Katz et al. (2001). A novel serine protease inhibition motif involving a multi-centered short hydrogen bonding network at the active site. J Mol Biol, 307, 1451-1486. PubMed id: 11292354 DOI: 10.1006/jmbi.2001.4516
22-Jan-01     Release date:   22-Jan-02    
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Protein chain
Pfam   ArchSchema ?
P00734  (THRB_HUMAN) -  Prothrombin
622 a.a.
36 a.a.
Protein chain
Pfam   ArchSchema ?
P00734  (THRB_HUMAN) -  Prothrombin
622 a.a.
250 a.a.
Protein chain
Pfam   ArchSchema ?
P28504  (HIR2_HIRME) -  Hirudin-2
65 a.a.
11 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 1 residue position (black cross)

 Enzyme reactions 
   Enzyme class: Chains L, H: E.C.  - Thrombin.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: Preferential cleavage: Arg-|-Gly; activates fibrinogen to fibrin and releases fibrinopeptide A and B.
 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     extracellular region   1 term 
  Biological process     blood coagulation   2 terms 
  Biochemical function     catalytic activity     3 terms  


DOI no: 10.1006/jmbi.2001.4516 J Mol Biol 307:1451-1486 (2001)
PubMed id: 11292354  
A novel serine protease inhibition motif involving a multi-centered short hydrogen bonding network at the active site.
B.A.Katz, K.Elrod, C.Luong, M.J.Rice, R.L.Mackman, P.A.Sprengeler, J.Spencer, J.Hataye, J.Janc, J.Link, J.Litvak, R.Rai, K.Rice, S.Sideris, E.Verner, W.Young.
We describe a new serine protease inhibition motif in which binding is mediated by a cluster of very short hydrogen bonds (<2.3 A) at the active site. This protease-inhibitor binding paradigm is observed at high resolution in a large set of crystal structures of trypsin, thrombin, and urokinase-type plasminogen activator (uPA) bound with a series of small molecule inhibitors (2-(2-phenol)indoles and 2-(2-phenol)benzimidazoles). In each complex there are eight enzyme-inhibitor or enzyme-water-inhibitor hydrogen bonds at the active site, three of which are very short. These short hydrogen bonds connect a triangle of oxygen atoms comprising O(gamma)(Ser195), a water molecule co-bound in the oxyanion hole (H(2)O(oxy)), and the phenolate oxygen atom of the inhibitor (O6'). Two of the other hydrogen bonds between the inhibitor and active site of the trypsin and uPA complexes become short in the thrombin counterparts, extending the three-centered short hydrogen-bonding array into a tetrahedral array of atoms (three oxygen and one nitrogen) involved in short hydrogen bonds. In the uPA complexes, the extensive hydrogen-bonding interactions at the active site prevent the inhibitor S1 amidine from forming direct hydrogen bonds with Asp189 because the S1 site is deeper in uPA than in trypsin or thrombin.Ionization equilibria at the active site associated with inhibitor binding are probed through determination and comparison of structures over a wide range of pH (3.5 to 11.4) of thrombin complexes and of trypsin complexes in three different crystal forms. The high-pH trypsin-inhibitor structures suggest that His57 is protonated at pH values as high as 9.5. The pH-dependent inhibition of trypsin, thrombin, uPA and factor Xa by 2-(2-phenol)benzimidazole analogs in which the pK(a) of the phenol group is modulated is shown to be consistent with a binding process involving ionization of both the inhibitor and the enzyme. These data further suggest that the pK(a) of His57 of each protease in the unbound state in solution is about the same, approximately 6.8. By comparing inhibition constants (K(i) values), inhibitor solubilities, inhibitor conformational energies and corresponding structures of short and normal hydrogen bond-mediated complexes, we have estimated the contribution of the short hydrogen bond networks to inhibitor affinity ( approximately 1.7 kcal/mol). The structures and K(i) values associated with the short hydrogen-bonding motif are compared with those corresponding to an alternate, Zn(2+)-mediated inhibition motif at the active site. Structural differences among apo-enzymes, enzyme-inhibitor and enzyme-inhibitor-Zn(2+) complexes are discussed in the context of affinity determinants, selectivity development, and structure-based inhibitor design.
  Selected figure(s)  
Figure 4.
Figure 4. Chemical structures of serine protease inhibitor analogs of APC-1144 that (A) make or (B) do not make short hydrogen bonds at the active site.
Figure 6.
Figure 6. (a) Structure and (2|F[o]| - |F[c]|), a[c] map contoured at 1.0 and 2.4s for P2[1]2[1]2[1] (form b) trypsin-APC-1144-Zn2+, pH 8.10, 1.37 Å resolution. Coordinate bonds to the Zn2+ are cyan, and hydrogen bonds are white. (b) Superposition of trypsin-APC-1144-Zn2+ (standard atom coloring scheme) onto trypsin-APC-1144 (carbon, cyan; oxygen, orange; and nitrogen, pink) shows a considerable change in the position and orientation of the phenol ring of the inhibitor. Coordinate and hydrogen bonds in the former are yellow, hydrogen bonds in the latter are cyan.
  The above figures are reprinted by permission from Elsevier: J Mol Biol (2001, 307, 1451-1486) copyright 2001.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
  21491494 T.Yang, J.C.Wu, C.Yan, Y.Wang, R.Luo, M.B.Gonzales, K.N.Dalby, and P.Ren (2011).
Virtual screening using molecular simulations.
  Proteins, 79, 1940-1951.  
20136072 J.W.Ponder, C.Wu, P.Ren, V.S.Pande, J.D.Chodera, M.J.Schnieders, I.Haque, D.L.Mobley, D.S.Lambrecht, R.A.DiStasio, M.Head-Gordon, G.N.Clark, M.E.Johnson, and T.Head-Gordon (2010).
Current status of the AMOEBA polarizable force field.
  J Phys Chem B, 114, 2549-2564.  
20148287 O.Nicolotti, I.Giangreco, T.F.Miscioscia, M.Convertino, F.Leonetti, L.Pisani, and A.Carotti (2010).
Screening of benzamidine-based thrombin inhibitors via a linear interaction energy in continuum electrostatics model.
  J Comput Aided Mol Des, 24, 117-129.  
19275144 C.Mulakala, and Y.N.Kaznessis (2009).
Path-integral method for predicting relative binding affinities of protein-ligand complexes.
  J Am Chem Soc, 131, 4521-4528.  
19399779 D.Jiao, J.Zhang, R.E.Duke, G.Li, M.J.Schnieders, and P.Ren (2009).
Trypsin-ligand binding free energies from explicit and implicit solvent simulations with polarizable potential.
  J Comput Chem, 30, 1701-1711.  
19965178 Y.Shi, D.Jiao, M.J.Schnieders, and P.Ren (2009).
Trypsin-ligand binding free energy calculation with AMOEBA.
  Conf Proc IEEE Eng Med Biol Soc, 1, 2328-2331.  
18427113 D.Jiao, P.A.Golubkov, T.A.Darden, and P.Ren (2008).
Calculation of protein-ligand binding free energy by using a polarizable potential.
  Proc Natl Acad Sci U S A, 105, 6290-6295.  
17013633 G.Mlinsek, M.Oblak, M.Hodoscek, and T.Solmajer (2007).
Thrombin inhibitors with novel P1 binding pocket functionality: free energy of binding analysis.
  J Mol Model, 13, 247-254.  
16700049 C.A.Bottoms, T.A.White, and J.J.Tanner (2006).
Exploring structurally conserved solvent sites in protein families.
  Proteins, 64, 404-421.  
12962630 J.R.Somoza, J.D.Ho, C.Luong, M.Ghate, P.A.Sprengeler, K.Mortara, W.D.Shrader, D.Sperandio, H.Chan, M.E.McGrath, and B.A.Katz (2003).
The structure of the extracellular region of human hepsin reveals a serine protease domain and a novel scavenger receptor cysteine-rich (SRCR) domain.
  Structure, 11, 1123-1131.
PDB code: 1p57
11731301 B.A.Katz, P.A.Sprengeler, C.Luong, E.Verner, K.Elrod, M.Kirtley, J.Janc, J.R.Spencer, J.G.Breitenbucher, H.Hui, D.McGee, D.Allen, A.Martelli, and R.L.Mackman (2001).
Engineering inhibitors highly selective for the S1 sites of Ser190 trypsin-like serine protease drug targets.
  Chem Biol, 8, 1107-1121.
PDB codes: 1gj4 1gj5 1gj6 1gj7 1gj8 1gj9 1gja 1gjb 1gjc 1gjd
11459634 R.Rai, A.Kolesnikov, Y.Li, W.B.Young, E.Leahy, P.A.Sprengeler, E.Verner, W.D.Shrader, J.Burgess-Henry, J.C.Sangalang, D.Allen, X.Chen, B.A.Katz, C.Luong, K.Elrod, and L.Cregar (2001).
Development of potent and selective factor Xa inhibitors.
  Bioorg Med Chem Lett, 11, 1797-1800.  
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 code is shown on the right.