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(-) Description

Title :  CRYSTAL STRUCTURE ANALYSIS OF CRUZAIN WITH THREE FRAGMENTS: 1 (N-(1H-BENZIMIDAZOL-2-YL)-1,3-DIMETHYL-PYRAZOLE-4-CARBOXAMIDE), 6 (2-AMINO-4,6-DIFLUOROBENZOTHIAZOLE) AND 9 (N-(1H-BENZIMIDAZOL-2-YL)-3-(4-FLUOROPHENYL)-1H-PYRAZOLE-4-CARBOXAMIDE).
 
Authors :  A. Tochowicz, J. H. Mckerrow, C. S. Craik
Date :  17 Aug 14  (Deposition) - 08 Apr 15  (Release) - 08 Apr 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.27
Chains :  Asym. Unit :  A,B,C,D,E
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  C  (1x)
Biol. Unit 4:  D  (1x)
Biol. Unit 5:  E  (1x)
Keywords :  Cysteine Protease, Cruzain, Fragments-Based Drug Discovery, Mutagenesis, Spr, Hydrolase-Hydrolase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. Tochowicz, G. M. Lee, M. R. Arkin, J. Neitz, J. Mckerrow, C. S. Craik
Applying Fragments Based- Drug Design To Identify Multiple Binding Modes On Cysteine Protease.
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - CRUZIPAIN
    Chains: A, B, C, D, E
    EC Number: 3.4.22.51
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: UNP RESIDUES 122-337
    Mutation: YES
    Organism Scientific: TRYPANOSOMA CRUZI
    Organism Taxid: 5693
    Synonym: CRUZAINE,MAJOR CYSTEINE PROTEINASE

 Structural Features

(-) Chains, Units

  12345
Asymmetric Unit : ABCDE
Biological Unit 1 (1x): A    
Biological Unit 2 (1x):  B   
Biological Unit 3 (1x):   C  
Biological Unit 4 (1x):    D 
Biological Unit 5 (1x):     E

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 6)

Asymmetric Unit (3, 6)
No.NameCountTypeFull Name
13H52Ligand/IonN-(1H-BENZIMIDAZOL-2-YL)-1,3-DIMETHYL-1H-PYRAZOLE-4-CARBOXAMIDE
23H61Ligand/IonN-(1H-BENZIMIDAZOL-2-YL)-3-(4-FLUOROPHENYL)-1H-PYRAZOLE-4-CARBOXAMIDE
33H73Ligand/Ion4,6-DIFLUORO-1,3-BENZOTHIAZOL-2-AMINE
Biological Unit 1 (2, 2)
No.NameCountTypeFull Name
13H51Ligand/IonN-(1H-BENZIMIDAZOL-2-YL)-1,3-DIMETHYL-1H-PYRAZOLE-4-CARBOXAMIDE
23H61Ligand/IonN-(1H-BENZIMIDAZOL-2-YL)-3-(4-FLUOROPHENYL)-1H-PYRAZOLE-4-CARBOXAMIDE
33H7-1Ligand/Ion4,6-DIFLUORO-1,3-BENZOTHIAZOL-2-AMINE
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
13H5-1Ligand/IonN-(1H-BENZIMIDAZOL-2-YL)-1,3-DIMETHYL-1H-PYRAZOLE-4-CARBOXAMIDE
23H6-1Ligand/IonN-(1H-BENZIMIDAZOL-2-YL)-3-(4-FLUOROPHENYL)-1H-PYRAZOLE-4-CARBOXAMIDE
33H71Ligand/Ion4,6-DIFLUORO-1,3-BENZOTHIAZOL-2-AMINE
Biological Unit 3 (2, 2)
No.NameCountTypeFull Name
13H51Ligand/IonN-(1H-BENZIMIDAZOL-2-YL)-1,3-DIMETHYL-1H-PYRAZOLE-4-CARBOXAMIDE
23H6-1Ligand/IonN-(1H-BENZIMIDAZOL-2-YL)-3-(4-FLUOROPHENYL)-1H-PYRAZOLE-4-CARBOXAMIDE
33H71Ligand/Ion4,6-DIFLUORO-1,3-BENZOTHIAZOL-2-AMINE
Biological Unit 4 (1, 1)
No.NameCountTypeFull Name
13H5-1Ligand/IonN-(1H-BENZIMIDAZOL-2-YL)-1,3-DIMETHYL-1H-PYRAZOLE-4-CARBOXAMIDE
23H6-1Ligand/IonN-(1H-BENZIMIDAZOL-2-YL)-3-(4-FLUOROPHENYL)-1H-PYRAZOLE-4-CARBOXAMIDE
33H71Ligand/Ion4,6-DIFLUORO-1,3-BENZOTHIAZOL-2-AMINE
Biological Unit 5 (0, 0)
No.NameCountTypeFull Name
13H5-1Ligand/IonN-(1H-BENZIMIDAZOL-2-YL)-1,3-DIMETHYL-1H-PYRAZOLE-4-CARBOXAMIDE
23H6-1Ligand/IonN-(1H-BENZIMIDAZOL-2-YL)-3-(4-FLUOROPHENYL)-1H-PYRAZOLE-4-CARBOXAMIDE
33H7-1Ligand/Ion4,6-DIFLUORO-1,3-BENZOTHIAZOL-2-AMINE

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLY A:20 , MET A:145binding site for residue 3H5 A 301
2AC2SOFTWAREGLY A:23 , SER A:25 , GLY A:65 , GLY A:66 , MET A:68 , ALA A:138 , ASP A:161 , THR D:146binding site for residue 3H6 A 302
3AC3SOFTWAREGLY B:23 , SER B:25 , GLY B:65 , GLY B:66 , ASP B:161 , HOH B:401binding site for residue 3H7 B 301
4AC4SOFTWAREGLY C:23 , SER C:25 , GLY C:65 , GLY C:66 , ASP C:161 , 3H5 C:302binding site for residue 3H7 C 301
5AC5SOFTWAREGLN C:19 , SER C:25 , MET C:145 , ASP C:161 , HIS C:162 , TRP C:184 , 3H7 C:301binding site for residue 3H5 C 302
6AC6SOFTWAREGLY D:23 , SER D:25 , GLY D:65 , GLY D:66 , ASP D:161binding site for residue 3H7 D 301

(-) SS Bonds  (15, 15)

Asymmetric Unit
No.Residues
1A:22 -A:63
2A:56 -A:101
3A:155 -A:203
4B:22 -B:63
5B:56 -B:101
6B:155 -B:203
7C:22 -C:63
8C:56 -C:101
9C:155 -C:203
10D:22 -D:63
11D:56 -D:101
12D:155 -D:203
13E:22 -E:63
14E:56 -E:101
15E:155 -E:203

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Ser C:61 -Gly C:62
2Val C:214 -Gly C:215

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4W5C)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4W5C)

(-) Exons   (0, 0)

(no "Exon" information available for 4W5C)

(-) Sequences/Alignments

Asymmetric Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
  Number of residues per labelling interval =   
  UniProt sequence: complete  aligned part    
   Show mapping: SCOP domains CATH domains Pfam domains Secondary structure (by author)
SAPs(SNPs) PROSITE motifs Exons
(details for a mapped element are shown in a popup box when the mouse pointer rests over it) 
Chain A from PDB  Type:PROTEIN  Length:215
                                                                                                                                                                                                                                                       
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......................hhhhhhhhhhhhhhhhhhh.......hhhhhhhh.........hhhhhhhhhhhh...eee.......hhhhh.......eeeeeeeeeeeeee...hhhhhhhhhhhhh.eeeeehhhhhh.....ee.........eeeeeeeee......eeeee...........eeeee...hhhhhhhh.eeeee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4w5c A   1 APAAVDWRARGAVTAVKDQGQCGSSWAFSAIGNVECQWFLAGHPLTNLSEQMLVSCDKTDSGCSGGLMNNAFEWIVQENNGAVYTEDSYPYASGEGISPPCTTSGHTVGATITGHVELPQDEAQIAAWLAVNGPVAVAVDASSWMTYTGGVMTSCVSEQLDHGVLLVGYNDSAAVPYWIIKNSWTTQWGEEGYIRIAKGSNQCLVKEEASSAVVG 215
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210     


Chain B from PDB  Type:PROTEIN  Length:215
                                                                                                                                                                                                                                                       
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eee.................hhhhhhhhhhhhhhhhh.........hhhhhhhh...hhhhh.hhhhhhhhhhhh...eee.......hhhhh.......eeeeeeee..eeeee..hhhhhhhhhhhhh.eeeeehhhhh......ee.........eeeeeeeee......eeeee...........eeeee...hhhhhhheeeeee.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4w5c B   1 APAAVDWRARGAVTAVKDQGQCGSSWAFSAIGNVECQWFLAGHPLTNLSEQMLVSCDKTDSGCSGGLMNNAFEWIVQENNGAVYTEDSYPYASGEGISPPCTTSGHTVGATITGHVELPQDEAQIAAWLAVNGPVAVAVDASSWMTYTGGVMTSCVSEQLDHGVLLVGYNDSAAVPYWIIKNSWTTQWGEEGYIRIAKGSNQCLVKEEASSAVVG 215
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210     


Chain C from PDB  Type:PROTEIN  Length:215
                                                                                                                                                                                                                                                       
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eee.................hhhhhhhhhhhhhhhhhhh.......hhhhhhhh.........hhhhhhhhhhhh...eee...................eeeeeeeeeeeeeee..hhhhhhhhhhhhh.eeeeehhhhhh.....ee.........eeeeeeeee......eeeee...........eeeee...hhhhhhhheeeeee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4w5c C   1 APAAVDWRARGAVTAVKDQGQCGSSWAFSAIGNVECQWFLAGHPLTNLSEQMLVSCDKTDSGCSGGLMNNAFEWIVQENNGAVYTEDSYPYASGEGISPPCTTSGHTVGATITGHVELPQDEAQIAAWLAVNGPVAVAVDASSWMTYTGGVMTSCVSEQLDHGVLLVGYNDSAAVPYWIIKNSWTTQWGEEGYIRIAKGSNQCLVKEEASSAVVG 215
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210     


Chain D from PDB  Type:PROTEIN  Length:215
                                                                                                                                                                                                                                                       
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eee.................hhhhhhhhhhhhhhhhh.........hhhhhhhh.........hhhhhhhhhhhh...eee.......................eeeeeeeeee...hhhhhhhhhhhhh.eeeeehhhhhh.....ee.........eeeeeeeee......eeeee...........eeeee...hhhhh....eeeee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4w5c D   1 APAAVDWRARGAVTAVKDQGQCGSSWAFSAIGNVECQWFLAGHPLTNLSEQMLVSCDKTDSGCSGGLMNNAFEWIVQENNGAVYTEDSYPYASGEGISPPCTTSGHTVGATITGHVELPQDEAQIAAWLAVNGPVAVAVDASSWMTYTGGVMTSCVSEQLDHGVLLVGYNDSAAVPYWIIKNSWTTQWGEEGYIRIAKGSNQCLVKEEASSAVVG 215
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210     


Chain E from PDB  Type:PROTEIN  Length:215
                                                                                                                                                                                                                                                       
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eee....................hhhhhhhhhhhhhh.........hhhhhhhh.........hhhhhhhhhhhh...eee.......hhhhh...........eeeeeeeeeee..hhhhhhhhhhhhh.eeeee...........ee.........eeeeeeeee......eeeee...........eeeee...hhhhhhhheeeeee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4w5c E   1 APAAVDWRARGAVTAVKDQGQCGSSWAFSAIGNVECQWFLAGHPLTNLSEQMLVSCDKTDSGCSGGLMNNAFEWIVQENNGAVYTEDSYPYASGEGISPPCTTSGHTVGATITGHVELPQDEAQIAAWLAVNGPVAVAVDASSWMTYTGGVMTSCVSEQLDHGVLLVGYNDSAAVPYWIIKNSWTTQWGEEGYIRIAKGSNQCLVKEEASSAVVG 215
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210
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  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (0, 0)

(no "SCOP Domain" information available for 4W5C)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4W5C)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4W5C)

(-) Gene Ontology  (5, 5)

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  CYSP_TRYCR | P25779
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        CYSP_TRYCR | P25779: 1aim 1ewl 1ewm 1ewo 1ewp 1f29 1f2a 1f2b 1f2c 1me3 1me4 1u9q 2aim 2oz2 3hd3 3i06 3iut 3kku 3lxs 4klb 4pi3 4qh6 4w5b 4xui

(-) Related Entries Specified in the PDB File

3kku 4pi3 4pi4 4w5b