1T31 - JenaLib

Title :   A DUAL INHIBITOR OF THE LEUKOCYTE PROTEASES CATHEPSIN G AND CHYMASE WITH THERAPEUTIC EFFICACY IN ANIMALS MODELS OF INFLAMMATION

Authors :   L. De Garavilla, M. N. Greco, E. C. Giardino, G. I. Wells, B. J. Haertlei J. A. Kauffman, T. W. Corcoran, C. K. Derian, A. J. Eckardt, W. M. Abraha N. Sukumar, Z. Chen, A. O. Pineda, F. S. Mathews, E. Di Cera, P. Andrade B. P. Damiano, B. E. Maryanoff, P. J. B. Pereira, Z. M. Wang, H. Rubin, R. W. Bode, N. M. Schechter, S. Strobl

Date :   23 Apr 04 (Deposition) - 01 Mar 05 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.90

Chains :   Asym. Unit : A
Biol. Unit 1: A  (1x)
Biol. Unit 2: A  (2x)

Keywords :   Human Chymase, Serine Proteinase, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   L. De Garavilla, M. N. Greco, N. Sukumar, Z. W. Chen, A. O. Pineda, F. S. Mathews, E. Di Cera, E. C. Giardino, G. I. Wells, B. J. Haertlein, J. A. Kauffman, T. W. Corcoran, C. K. Derian, A. J. Eckardt, B. P. Damiano, P. Andrade-Gordon, B. E. Maryanoff
A Novel, Potent Dual Inhibitor Of The Leukocyte Proteases Cathepsin G And Chymase: Molecular Mechanisms And Anti-Inflammatory Activity In Vivo.
J. Biol. Chem. V. 280 18001 2005
PubMed-ID: 15741158 | Reference-DOI: 10.1074/JBC.M501302200

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (5, 13)

Asymmetric Unit (5, 13)

No.	Name	Count	Type	Full Name
1	CO	1	Ligand/Ion	COBALT (II) ION
2	MES	1	Ligand/Ion	2-(N-MORPHOLINO)-ETHANESULFONIC ACID
3	NAG	3	Ligand/Ion	N-ACETYL-D-GLUCOSAMINE
4	OHH	1	Ligand/Ion	2-[3-({METHYL[1-(2-NAPHTHOYL)PIPERIDIN-4-YL]AMINO}CARBONYL)-2-NAPHTHYL]-1-(1-NAPHTHYL)-2-OXOETHYLPHOSPHONIC ACID
5	SO4	7	Ligand/Ion	SULFATE ION

Biological Unit 1 (4, 12)

No.	Name	Count	Type	Full Name
1	CO	-1	Ligand/Ion	COBALT (II) ION
2	MES	1	Ligand/Ion	2-(N-MORPHOLINO)-ETHANESULFONIC ACID
3	NAG	3	Ligand/Ion	N-ACETYL-D-GLUCOSAMINE
4	OHH	1	Ligand/Ion	2-[3-({METHYL[1-(2-NAPHTHOYL)PIPERIDIN-4-YL]AMINO}CARBONYL)-2-NAPHTHYL]-1-(1-NAPHTHYL)-2-OXOETHYLPHOSPHONIC ACID
5	SO4	7	Ligand/Ion	SULFATE ION

Biological Unit 2 (4, 24)

No.	Name	Count	Type	Full Name
1	CO	-1	Ligand/Ion	COBALT (II) ION
2	MES	2	Ligand/Ion	2-(N-MORPHOLINO)-ETHANESULFONIC ACID
3	NAG	6	Ligand/Ion	N-ACETYL-D-GLUCOSAMINE
4	OHH	2	Ligand/Ion	2-[3-({METHYL[1-(2-NAPHTHOYL)PIPERIDIN-4-YL]AMINO}CARBONYL)-2-NAPHTHYL]-1-(1-NAPHTHYL)-2-OXOETHYLPHOSPHONIC ACID
5	SO4	14	Ligand/Ion	SULFATE ION

Sites (13, 13)

Asymmetric Unit (13, 13)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	ASN A:72 , THR A:74 , GLU A:75 , THR A:154 , NAG A:303	BINDING SITE FOR RESIDUE NAG A 301
02	AC2	SOFTWARE	NAG A:301	BINDING SITE FOR RESIDUE NAG A 303
03	AC3	SOFTWARE	ASN A:95 , HOH A:1123 , HOH A:1214 , HOH A:1215 , HOH A:1219	BINDING SITE FOR RESIDUE NAG A 302
04	AC4	SOFTWARE	LEU A:114 , THR A:115 , LEU A:116	BINDING SITE FOR RESIDUE SO4 A 902
05	AC5	SOFTWARE	PHE A:41 , ARG A:143 , PRO A:150 , GLY A:151 , HOH A:1187 , HOH A:1197	BINDING SITE FOR RESIDUE SO4 A 903
06	AC6	SOFTWARE	LYS A:93 , HIS A:100 , HIS A:101 , HOH A:1070 , HOH A:1193	BINDING SITE FOR RESIDUE SO4 A 904
07	AC7	SOFTWARE	MET A:135 , ARG A:161 , ASN A:185 , LYS A:186 , HOH A:1072 , HOH A:1218	BINDING SITE FOR RESIDUE SO4 A 905
08	AC8	SOFTWARE	PRO A:38 , SER A:39 , ARG A:174	BINDING SITE FOR RESIDUE SO4 A 906
09	AC9	SOFTWARE	THR A:20 , GLU A:21	BINDING SITE FOR RESIDUE SO4 A 907
10	BC1	SOFTWARE	ARG A:137 , ALA A:202 , HOH A:1125 , HOH A:1175	BINDING SITE FOR RESIDUE SO4 A 908
11	BC2	SOFTWARE	HIS A:25 , GLU A:78 , HOH A:1002 , HOH A:1005	BINDING SITE FOR RESIDUE CO A 909
12	BC3	SOFTWARE	LYS A:40 , HIS A:57 , GLN A:166 , PRO A:185A , ARG A:185B , ALA A:190 , PHE A:191 , LYS A:192 , GLY A:193 , SER A:195 , SER A:214 , TYR A:215 , GLY A:216 , ARG A:217 , SER A:218 , ALA A:226 , HOH A:1040 , HOH A:1046 , HOH A:1107 , HOH A:1154 , HOH A:1209 , HOH A:1216	BINDING SITE FOR RESIDUE OHH A 901
13	BC4	SOFTWARE	TYR A:32 , GLU A:34 , THR A:67 , ILE A:73 , TRP A:80 , LYS A:82 , HOH A:1034 , HOH A:1085 , HOH A:1130	BINDING SITE FOR RESIDUE MES A 910

SS Bonds (3, 3)

Cis Peptide Bonds (1, 1)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (3, 3)

Asymmetric Unit (3, 3)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_011770	G	46	R	CMA1_HUMAN	Polymorphism	5246	A	G	37	R
2	UniProt	VAR_011771	H	66	R	CMA1_HUMAN	Polymorphism	5247	A	H	57	R
3	UniProt	VAR_029190	R	98	H	CMA1_HUMAN	Polymorphism	13306252	A	R	90	H

SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

Biological Unit 1 (3, 3)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_011770	G	46	R	CMA1_HUMAN	Polymorphism	5246	A	G	37	R
2	UniProt	VAR_011771	H	66	R	CMA1_HUMAN	Polymorphism	5247	A	H	57	R
3	UniProt	VAR_029190	R	98	H	CMA1_HUMAN	Polymorphism	13306252	A	R	90	H

SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

Biological Unit 2 (3, 6)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_011770	G	46	R	CMA1_HUMAN	Polymorphism	5246	A	G	37	R
2	UniProt	VAR_011771	H	66	R	CMA1_HUMAN	Polymorphism	5247	A	H	57	R
3	UniProt	VAR_029190	R	98	H	CMA1_HUMAN	Polymorphism	13306252	A	R	90	H

SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

PROSITE Motifs (3, 3)

Asymmetric Unit (3, 3)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	TRYPSIN_DOM	PS50240	Serine proteases, trypsin domain profile.	CMA1_HUMAN	22-245	1	A:16-243
2	TRYPSIN_HIS	PS00134	Serine proteases, trypsin family, histidine active site.	CMA1_HUMAN	62-67	1	A:53-58
3	TRYPSIN_SER	PS00135	Serine proteases, trypsin family, serine active site.	CMA1_HUMAN	197-208	1	A:189-200

Biological Unit 1 (3, 3)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	TRYPSIN_DOM	PS50240	Serine proteases, trypsin domain profile.	CMA1_HUMAN	22-245	1	A:16-243
2	TRYPSIN_HIS	PS00134	Serine proteases, trypsin family, histidine active site.	CMA1_HUMAN	62-67	1	A:53-58
3	TRYPSIN_SER	PS00135	Serine proteases, trypsin family, serine active site.	CMA1_HUMAN	197-208	1	A:189-200

Biological Unit 2 (3, 6)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	TRYPSIN_DOM	PS50240	Serine proteases, trypsin domain profile.	CMA1_HUMAN	22-245	2	A:16-243
2	TRYPSIN_HIS	PS00134	Serine proteases, trypsin family, histidine active site.	CMA1_HUMAN	62-67	2	A:53-58
3	TRYPSIN_SER	PS00135	Serine proteases, trypsin family, serine active site.	CMA1_HUMAN	197-208	2	A:189-200

Exons (4, 4)

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:226
 aligned with CMA1_HUMAN | P23946 from UniProtKB/Swiss-Prot  Length:247

    Alignment length:226
                                    31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241      
          CMA1_HUMAN     22 IIGGTECKPHSRPYMAYLEIVTSNGPSKFCGGFLIRRNFVLTAAHCAGRSITVTLGAHNITEEEDTWQKLEVIKQFRHPKYNTSTLHHDIMLLKLKEKASLTLAVGTLPFPSQFNFVPPGRMCRVAGWGRTGVLKPGSDTLQEVKLRLMDPQACSHFRDFDHNLQLCVGNPRKTKSAFKGDSGGPLLCAGVAQGIVSYGRSDAKPPAVFTRISHYRPWINQILQAN  247
               SCOP domains d1t31a_ A: Chymase (mast cell protease I)                                                                                                                                                                                          SCOP domains
               CATH domains 1t31A01     1t31A02 A:28-120,A:233-245 Trypsin-like serine proteases                                       1t31A01 A:16-27,A:121-232 Trypsin-like serine proteases                                                   1t31A02       CATH domains
               Pfam domains Trypsin-1t31A01 A:16-238                                                                                                                                                                                                   ------- Pfam domains
         Sec.struct. author ....ee........eeeeeee......eeeeeeeee..eeeehhhhh..eeeeee............eeeeeeeeee.............eeeee..........................eeeeee..............eeeeeeeehhhhhh.........eeee................eeee..eeeeeeee........eeeee...hhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------R-------------------R-------------------------------H----------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) TRYPSIN_DOM  PDB: A:16-243 UniProt: 22-245                                                                                                                                                                                      -- PROSITE (1)
                PROSITE (2) ----------------------------------------TRYPSI---------------------------------------------------------------------------------------------------------------------------------TRYPSIN_SER --------------------------------------- PROSITE (2)
           Transcript 1 (1) Exon 1.2a  PDB: A:16-61 UniProt: 20-70           ---------------------------------------------Exon 1.4a  PDB: A:108-192 (gaps) UniProt: 116-200                                    Exon 1.5b  PDB: A:193-245 (gaps)                Transcript 1 (1)
           Transcript 1 (2) ------------------------------------------------Exon 1.3  PDB: A:61-107 (gaps) UniProt: 70-115------------------------------------------------------------------------------------------------------------------------------------ Transcript 1 (2)
                1t31 A   16 IIGGTECKPHSRPYMAYLEIVTSNGPSKFCGGFLIRRNFVLTAAHCAGRSITVTLGAHNITEEEDTWQKLEVIKQFRHPKYNTSTLHHDIMLLKLKEKASLTLAVGTLPFPSQKNFVPPGRMCRVAGWGRTGVLKPGSDTLQEVKLRLMDPQACSHFRDFDHNLQLCVGNPRKTKSAFKGDSGGPLLCAGAAQGIVSYGRSDAKPPAVFTRISHYQPWINQILQAN  245
                                    25        35 |||    42        52        63        73 ||  |  83        93       103       113       123       133       143    || 154       164    || 176 |     185||     193       207       217   ||  229       239      
                                               36A||                       61|          75|  |                                                                  148|                169|  177A     185A|              202|           221|                     
                                                36B|                        63           77  |                                                                   150                 172            185B               207            224                     
                                                 36C                                       79A

Legend:		→ Mismatch	(orange background)
	-	→ Gap	(green background, '-', border residues have a numbering label)
		→ Modified Residue	(blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
	x	→ Chemical Group	(purple background, 'x', labelled with number + name, e.g. ACE or NH2)
	extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '\|'

Classification and Annotation

SCOP Domains (1, 1)

CATH Domains (1, 2)

Pfam Domains (1, 1)

Gene Ontology (21, 21)

Asymmetric Unit(hide GO term definitions)

Chain A (CMA1_HUMAN | P23946)

molecular function
	GO:0004175	endopeptidase activity	Catalysis of the hydrolysis of internal, alpha-peptide bonds in a polypeptide chain.
	GO:0016787	hydrolase activity	Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
	GO:0008233	peptidase activity	Catalysis of the hydrolysis of a peptide bond. A peptide bond is a covalent bond formed when the carbon atom from the carboxyl group of one amino acid shares electrons with the nitrogen atom from the amino group of a second amino acid.
	GO:0042277	peptide binding	Interacting selectively and non-covalently with peptides, any of a group of organic compounds comprising two or more amino acids linked by peptide bonds.
	GO:0004252	serine-type endopeptidase activity	Catalysis of the hydrolysis of internal, alpha-peptide bonds in a polypeptide chain by a catalytic mechanism that involves a catalytic triad consisting of a serine nucleophile that is activated by a proton relay involving an acidic residue (e.g. aspartate or glutamate) and a basic residue (usually histidine).
	GO:0008236	serine-type peptidase activity	Catalysis of the hydrolysis of peptide bonds in a polypeptide chain by a catalytic mechanism that involves a catalytic triad consisting of a serine nucleophile that is activated by a proton relay involving an acidic residue (e.g. aspartate or glutamate) and a basic residue (usually histidine).
biological process
	GO:0002003	angiotensin maturation	The process leading to the attainment of the full functional capacity of angiotensin by conversion of renin substrate into mature angiotensin in the blood.
	GO:0071333	cellular response to glucose stimulus	Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a glucose stimulus.
	GO:0022617	extracellular matrix disassembly	A process that results in the breakdown of the extracellular matrix.
	GO:0006955	immune response	Any immune system process that functions in the calibrated response of an organism to a potential internal or invasive threat.
	GO:0050720	interleukin-1 beta biosynthetic process	The chemical reactions and pathways resulting in the formation of interleukin-1 beta.
	GO:0030901	midbrain development	The process whose specific outcome is the progression of the midbrain over time, from its formation to the mature structure. The midbrain is the middle division of the three primary divisions of the developing chordate brain or the corresponding part of the adult brain (in vertebrates, includes a ventral part containing the cerebral peduncles and a dorsal tectum containing the corpora quadrigemina and that surrounds the aqueduct of Sylvius connecting the third and fourth ventricles).
	GO:0006518	peptide metabolic process	The chemical reactions and pathways involving peptides, compounds of two or more amino acids where the alpha carboxyl group of one is bound to the alpha amino group of another.
	GO:0045766	positive regulation of angiogenesis	Any process that activates or increases angiogenesis.
	GO:0016485	protein processing	Any protein maturation process achieved by the cleavage of a peptide bond or bonds within a protein. Protein maturation is the process leading to the attainment of the full functional capacity of a protein.
	GO:0006508	proteolysis	The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds.
	GO:0050727	regulation of inflammatory response	Any process that modulates the frequency, rate or extent of the inflammatory response, the immediate defensive reaction (by vertebrate tissue) to infection or injury caused by chemical or physical agents.
cellular component
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
	GO:0031012	extracellular matrix	A structure lying external to one or more cells, which provides structural support for cells or tissues.
	GO:0005576	extracellular region	The space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane. This term covers the host cell environment outside an intracellular parasite.
	GO:0043231	intracellular membrane-bounded organelle	Organized structure of distinctive morphology and function, bounded by a single or double lipid bilayer membrane and occurring within the cell. Includes the nucleus, mitochondria, plastids, vacuoles, and vesicles. Excludes the plasma membrane.

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	1t31
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