4UY1 - JenaLib

Title :   NOVEL PYRAZOLE SERIES OF GROUP X SECRETORY PHOSPHOLIPASE A2 (SPLA2-X) INHIBITORS

Authors :   J. Sandmark, L. Oster, K. Hallberg, C. Bodin, H. Chen

Date :   28 Aug 14 (Deposition) - 15 Oct 14 (Release) - 17 Dec 14 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.20

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

Keywords :   Hydrolase, Fragment Based Lead Generation, Virtual Screening, Drug Discovery (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   H. Chen, L. Knerr, T. Akerud, K. Hallberg, C. Bodin, L. Oster, M. Rohman K. Osterlund, H. G. Beisel, T. Olsson, J. Brengdhal, J. Sandmark
Discovery Of A Novel Pyrazole Series Of Group X Secreted Phospholipase A2 Inhibitor (Spla2X) Via Fragment Based Virtual Screening
Bioorg. Med. Chem. Lett. V. 24 5251 2014
PubMed-ID: 25316315 | Reference-DOI: 10.1016/J.BMCL.2014.09.058

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (5, 20)

Asymmetric Unit (5, 20)

No.	Name	Count	Type	Full Name
1	1PE	3	Ligand/Ion	PENTAETHYLENE GLYCOL
2	CA	2	Ligand/Ion	CALCIUM ION
3	DMS	7	Ligand/Ion	DIMETHYL SULFOXIDE
4	PEG	6	Ligand/Ion	DI(HYDROXYETHYL)ETHER
5	TJM	2	Ligand/Ion	5-(2,5-DIMETHYL-3-THIENYL)-1H-PYRAZOLE-3-CARBOXAMIDE

Biological Unit 1 (4, 10)

No.	Name	Count	Type	Full Name
1	1PE	2	Ligand/Ion	PENTAETHYLENE GLYCOL
2	CA	-1	Ligand/Ion	CALCIUM ION
3	DMS	4	Ligand/Ion	DIMETHYL SULFOXIDE
4	PEG	3	Ligand/Ion	DI(HYDROXYETHYL)ETHER
5	TJM	1	Ligand/Ion	5-(2,5-DIMETHYL-3-THIENYL)-1H-PYRAZOLE-3-CARBOXAMIDE

Biological Unit 2 (4, 8)

No.	Name	Count	Type	Full Name
1	1PE	1	Ligand/Ion	PENTAETHYLENE GLYCOL
2	CA	-1	Ligand/Ion	CALCIUM ION
3	DMS	3	Ligand/Ion	DIMETHYL SULFOXIDE
4	PEG	3	Ligand/Ion	DI(HYDROXYETHYL)ETHER
5	TJM	1	Ligand/Ion	5-(2,5-DIMETHYL-3-THIENYL)-1H-PYRAZOLE-3-CARBOXAMIDE

Sites (20, 20)

Asymmetric Unit (20, 20)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	PHE A:26 , GLY A:28 , GLY A:30 , ASP A:47 , 1PE A:1125 , TJM A:1130	BINDING SITE FOR RESIDUE CA A 200
02	AC2	SOFTWARE	PHE B:26 , GLY B:28 , GLY B:30 , ASP B:47 , TJM B:1129 , HOH B:2008	BINDING SITE FOR RESIDUE CA B 200
03	AC3	SOFTWARE	ARG A:15 , TYR A:103 , LEU B:105 , LEU B:108	BINDING SITE FOR RESIDUE 1PE A1124
04	AC4	SOFTWARE	ILE A:2 , GLY A:28 , LEU A:29 , GLY A:30 , ASP A:47 , LYS A:61 , GLN A:72 , CA A:200 , TJM A:1130 , HOH A:2027 , HOH A:2067	BINDING SITE FOR RESIDUE 1PE A1125
05	AC5	SOFTWARE	LEU B:29 , HIS B:46 , ASP B:47 , TYR B:50 , LYS B:61 , GLN B:72 , SER B:73 , ASN B:96 , TJM B:1129 , HOH B:2008 , HOH B:2045	BINDING SITE FOR RESIDUE 1PE B1125
06	AC6	SOFTWARE	PRO A:78 , ALA A:79 , LEU B:75 , CYS B:76 , GLN B:92	BINDING SITE FOR RESIDUE DMS B1126
07	AC7	SOFTWARE	CYS A:76 , GLN A:92 , PRO B:78 , ALA B:79	BINDING SITE FOR RESIDUE DMS A1126
08	AC8	SOFTWARE	LYS B:22 , GLY B:24 , CYS B:27 , GLY B:28 , LEU B:29	BINDING SITE FOR RESIDUE DMS B1127
09	AC9	SOFTWARE	GLY A:24 , CYS A:25 , PHE A:26 , CYS A:27 , GLY A:28 , LEU A:29 , GLY A:30	BINDING SITE FOR RESIDUE DMS A1127
10	BC1	SOFTWARE	GLU A:54 , SER A:59 , PRO A:60 , LYS A:61 , LEU A:75 , HOH A:2055	BINDING SITE FOR RESIDUE DMS A1128
11	BC2	SOFTWARE	ASP A:47 , TYR A:50 , THR A:51 , GLU A:54	BINDING SITE FOR RESIDUE DMS A1129
12	BC3	SOFTWARE	ARG A:36 , TYR A:107 , TYR A:110 , GLY B:7	BINDING SITE FOR RESIDUE DMS B1128
13	BC4	SOFTWARE	LEU A:5 , PRO A:17 , TYR A:20 , PHE A:26 , GLY A:28 , CYS A:43 , HIS A:46 , ASP A:47 , CA A:200 , 1PE A:1125 , HOH A:2068	BINDING SITE FOR RESIDUE TJM A1130
14	BC5	SOFTWARE	ILE B:2 , LEU B:5 , ALA B:6 , PRO B:17 , TYR B:20 , MET B:21 , PHE B:26 , GLY B:28 , CYS B:43 , HIS B:46 , ASP B:47 , ILE B:94 , CA B:200 , 1PE B:1125	BINDING SITE FOR RESIDUE TJM B1129
15	BC6	SOFTWARE	TRP A:67 , GLN A:68 , CYS A:69 , PEG A:1132 , HOH A:2005	BINDING SITE FOR RESIDUE PEG A1131
16	BC7	SOFTWARE	ALA A:6 , GLY A:7 , GLY A:10 , CYS A:11 , PEG A:1131 , ARG B:36 , TYR B:107 , TYR B:110	BINDING SITE FOR RESIDUE PEG A1132
17	BC8	SOFTWARE	SER B:59 , PRO B:60 , LYS B:61 , VAL B:74 , GLN B:92 , ASN B:96	BINDING SITE FOR RESIDUE PEG B1130
18	BC9	SOFTWARE	LEU A:114 , LEU B:3 , GLU B:4 , ARG B:64 , TYR B:65 , TRP B:67 , HOH B:2024	BINDING SITE FOR RESIDUE PEG B1131
19	CC1	SOFTWARE	ARG A:64 , SER A:66 , PRO A:78 , GLU A:80 , GLN B:68 , LEU B:75	BINDING SITE FOR RESIDUE PEG A1133
20	CC2	SOFTWARE	ALA B:38 , TRP B:41 , CYS B:97 , GLN B:112	BINDING SITE FOR RESIDUE PEG B1132

SS Bonds (16, 16)

Cis Peptide Bonds (3, 3)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (0, 0)

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:122
                                                                                                                                                          
               SCOP domains -------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhh..hhhhhh...............hhhhhhhhhhhhhhhhhhhh..........eee....eee....hhhhhhhhhhhhhhhhhhhh...hhhh...hhhhh....... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------- Transcript
                 4uy1 A   1 GILELAGTVGCVGPRTPIAYMKYGCFCGLGGHGQPRDAIDWCCHGHDCCYTRAEEAGCSPKTERYSWQCVNQSVLCGPAENKCQELLCKCDQEIANCLAQTEYNLKYLFYPQFLCEPDSPKC 122
                                    10        20        30        40        50        60        70        80        90       100       110       120

Chain B from PDB  Type:PROTEIN  Length:123
                                                                                                                                                           
               SCOP domains --------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhh..hhhhhh...............hhhhhhhhhhhhhhhhhhhh..........eeee..eeee....hhhhhhhhhhhhhhhhhhhh...hhhh...hhhhh........ Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------- Transcript
                 4uy1 B   1 GILELAGTVGCVGPRTPIAYMKYGCFCGLGGHGQPRDAIDWCCHGHDCCYTRAEEAGCSPKTERYSWQCVNQSVLCGPAENKCQELLCKCDQEIANCLAQTEYNLKYLFYPQFLCEPDSPKCD 123
                                    10        20        30        40        50        60        70        80        90       100       110       120

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	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 (0, 0)

CATH Domains (0, 0)

Pfam Domains (0, 0)

Gene Ontology (26, 26)

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	Ligands, Modified Residues, Ions
		1PE	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
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	Sites
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	Cis Peptide Bonds
		Gly A:77 - Pro A:78	[ RasMol ]
		Gly B:13 - Pro B:14	[ RasMol ]
		Gly B:77 - Pro B:78	[ RasMol ]

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