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Asym./Biol. Unit - manually (Jmol Viewer)

Asym./Biol. Unit (Jmol Viewer)

Asym./Biol. Unit - sites (Jmol Viewer)

Title :   STRUCTURE-GUIDED DESIGN OF ALPHA-AMINO ACID-DERIVED PIN1 INHIBITORS

Authors :   L. M. Baker, P. Dokurno, D. A. Robinson, A. E. Surgenor, J. B. Murray, A. J. Potter, J. D. Moore

Date :   19 Oct 09 (Deposition) - 22 Dec 09 (Release) - 05 Jan 10 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.19

Chains :   Asym./Biol. Unit : A

Keywords :   Sbdd, Ppiase, Isomerase, Rotamase, Small Molecule, Proline Directed Kinase, Cell Cycle, Oncogenic Transformation, Nucleus, Phosphoprotein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   A. J. Potter, S. Ray, L. Gueritz, C. L. Nunns, C. J. Bryant, S. F. Scrace, N. Matassova, L. M. Baker, P. Dokurno, D. A. Robinson, A. E. Surgenor, B. Davis, J. B. Murray, C. M. Richardson, J. D. Moore
Structure-Guided Design Of Alpha-Amino Acid-Derived Pin1 Inhibitors
Bioorg. Med. Chem. Lett. V. 20 586 2010
PubMed-ID: 19969456 | Reference-DOI: 10.1016/J.BMCL.2009.11.090
(for further references see the PDB file header)

Molecule 1 - PEPTIDYL-PROLYL CIS-TRANS ISOMERASE NIMA- INTERACTING 1
	Chains	:	A
	EC Number	:	5.2.1.8
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET28A
	Expression System Strain	:	BL21 (DE3)
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Gene	:	PIN1
	Mutation	:	YES
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	ROTAMASE PIN1, PPIASE PIN1

		1
Asymmetric/Biological Unit	:	A

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (3, 3)

No.	Name	Count	Type	Full Name
1	12P	1	Ligand/Ion	DODECAETHYLENE GLYCOL
2	4BL	1	Ligand/Ion	6-METHYL-1H-INDOLE-2-CARBOXYLIC ACID
3	SO4	1	Ligand/Ion	SULFATE ION

Asymmetric Unit (3, 3)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	TYR A:23 , ALA A:31 , SER A:32 , TRP A:34 , ILE A:93 , LYS A:97 , SER A:98 , MET A:146 , HOH A:217 , HOH A:244	BINDING SITE FOR RESIDUE 12P A 164
2	AC2	SOFTWARE	LYS A:63 , ARG A:68 , ARG A:69 , SER A:154 , 4BL A:166 , HOH A:195	BINDING SITE FOR RESIDUE SO4 A 165
3	AC3	SOFTWARE	LEU A:61 , CYS A:113 , MET A:130 , GLN A:131 , PHE A:134 , SER A:154 , SO4 A:165 , HOH A:175	BINDING SITE FOR RESIDUE 4BL A 166

(no "SS Bond" information available for 3KAB)

(no "Cis Peptide Bond" information available for 3KAB)

(no "SAP(SNP)/Variant" information available for 3KAB)

Asymmetric/Biological Unit (3, 3)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	WW_DOMAIN_1	PS01159	WW/rsp5/WWP domain signature.	PIN1_HUMAN	11-37	1	A:11-37
2	PPIC_PPIASE_2	PS50198	PpiC-type peptidyl-prolyl cis-trans isomerase family profile.	PIN1_HUMAN	52-163	1	A:52-163
3	PPIC_PPIASE_1	PS01096	PpiC-type peptidyl-prolyl cis-trans isomerase signature.	PIN1_HUMAN	103-123	1	A:103-123

Asymmetric/Biological Unit (4, 4)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1a	ENST00000247970	1a	ENSE00000872705	chr19:9945999-9946078	80	PIN1_HUMAN	1-20	20	1	A:7-20	14
1.2	ENST00000247970	2	ENSE00000872706	chr19:9949112-9949324	213	PIN1_HUMAN	20-91	72	1	A:20-91 (gaps)	72
1.3a	ENST00000247970	3a	ENSE00000872707	chr19:9958706-9958816	111	PIN1_HUMAN	91-128	38	1	A:91-128	38
1.4a	ENST00000247970	4a	ENSE00000872708	chr19:9959766-9960358	593	PIN1_HUMAN	128-163	36	1	A:128-163	36

Asymmetric/Biological 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
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Chain A from PDB  Type:PROTEIN  Length:145
 aligned with PIN1_HUMAN | Q13526 from UniProtKB/Swiss-Prot  Length:163

    Alignment length:157
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       
           PIN1_HUMAN     7 LPPGWEKRMSRSSGRVYYFNHITNASQWERPSGNSSSGGKNGQGEPARVRCSHLLVKHSQSRRPSSWRQEKITRTKEEALELINGYIQKIKSGEEDFESLASQFSDCSSAKARGDLGAFSRGQMQKPFEDASFALRTGEMSGPVFTDSGIHIILRTE 163
               SCOP domains d3kaba1 A:7-38                  ------------d3kaba2 A:51-163 Mitotic rotamase PIN1, domain 2                                                                  SCOP domains
               CATH domains 3kabA01 A:7-37                 ----------------3kabA02 A:54-163  [code=3.10.50.40, no name defined]                                                           CATH domains
               Pfam domains WW-3kabA02 A:7-37              ---------------------Rotamase-3kabA01 A:59-163                                                                                 Pfam domains
         Sec.struct. author ....eeeee......eeeee.....ee.....------------...eeeeeeeee..................hhhhhhhhhhhhhhhhhhh..hhhhhhhhhh.hhhhhhh.eeeeee....hhhhhhhhhhh........eee..eeeeeeeee Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) ----WW_DOMAIN_1  PDB: A:11-37  --------------PPIC_PPIASE_2  PDB: A:52-163 UniProt: 52-163                                                                     PROSITE (1)
                PROSITE (2) ------------------------------------------------------------------------------------------------PPIC_PPIASE_1        ---------------------------------------- PROSITE (2)
           Transcript 1 (1) Exon 1.1a     ----------------------------------------------------------------------Exon 1.3a  PDB: A:91-128              ----------------------------------- Transcript 1 (1)
           Transcript 1 (2) -------------Exon 1.2  PDB: A:20-91 (gaps) UniProt: 20-91                            ------------------------------------Exon 1.4a  PDB: A:128-163            Transcript 1 (2)
                 3kab A   7 LPPGWEKAMSRSSGRVYYFNHITNASQWERPS------------EPARVRCSHLLVKHSQSRRPSSWRQEKITRTKEEALELINGYIQKIKSGEEDFESLASQFSDCSSAKARGDLGAFSRGQMQKPFEDASFALRTGEMSGPVFTDSGIHIILRTE 163
                                    16        26        36 |       -    |   56        66        76        86        96       106       116       126       136       146       156       
                                                          38           51

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 '\|'

Asymmetric/Biological Unit

Classes(

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Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: All beta proteins (24004)

Fold: WW domain-like (101)

Superfamily: WW domain (80)

Family: WW domain (69)

Protein domain: Mitotic rotamase PIN1 (37)

Human (Homo sapiens) [TaxId: 9606] (37)

d3kaba1

A:7-38

Class: Alpha and beta proteins (a+b) (23004)

Fold: FKBP-like (309)

Superfamily: FKBP-like (198)

Family: FKBP immunophilin/proline isomerase (153)

Protein domain: Mitotic rotamase PIN1, domain 2 (36)

Human (Homo sapiens) [TaxId: 9606] (35)

d3kaba2

A:51-163

Asymmetric/Biological Unit

Classes(

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Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

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Organisms( (-)

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Class: Alpha Beta (26913)

Architecture: Roll (3276)

Topology: Chitinase A; domain 3 (225)

Homologous Superfamily: [code=3.10.50.40, no name defined] (98)

Human (Homo sapiens) (72)

3kabA02

A:54-163

Class: Mainly Beta (13760)

Architecture: Single Sheet (341)

Topology: Ubiquitin Ligase Nedd4; Chain: W; (40)

Homologous Superfamily: [code=2.20.70.10, no name defined] (40)

Human (Homo sapiens) (27)

3kabA01

A:7-37

Asymmetric/Biological Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: FKBP (43)

Family: Rotamase (35)

Homo sapiens (Human) (28)

Rotamase-3kabA01

A:59-163

Clan: no clan defined [family: WW] (77)

Family: WW (77)

Homo sapiens (Human) (62)

WW-3kabA02

A:7-37

Asymmetric/Biological Unit(hide GO term definitions)

Chain A (PIN1_HUMAN | Q13526)

molecular function
	GO:0032794	GTPase activating protein binding	Interacting selectively and non-covalently with a GTPase activating protein.
	GO:0008013	beta-catenin binding	Interacting selectively and non-covalently with the beta subunit of the catenin complex.
	GO:0016853	isomerase activity	Catalysis of the geometric or structural changes within one molecule. Isomerase is the systematic name for any enzyme of EC class 5.
	GO:0031434	mitogen-activated protein kinase kinase binding	Interacting selectively and non-covalently with a mitogen-activated protein kinase kinase, any protein that can phosphorylate a MAP kinase.
	GO:0003774	motor activity	Catalysis of the generation of force resulting either in movement along a microfilament or microtubule, or in torque resulting in membrane scission, coupled to the hydrolysis of a nucleoside triphosphate.
	GO:0003755	peptidyl-prolyl cis-trans isomerase activity	Catalysis of the reaction: peptidyl-proline (omega=180) = peptidyl-proline (omega=0).
	GO:0050815	phosphoserine residue binding	Interacting selectively and non-covalently with a phosphorylated serine residue within a protein.
	GO:0050816	phosphothreonine residue binding	Interacting selectively and non-covalently with a phosphorylated threonine residue within a protein.
	GO:0005515	protein binding	Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
biological process
	GO:0007049	cell cycle	The progression of biochemical and morphological phases and events that occur in a cell during successive cell replication or nuclear replication events. Canonically, the cell cycle comprises the replication and segregation of genetic material followed by the division of the cell, but in endocycles or syncytial cells nuclear replication or nuclear division may not be followed by cell division.
	GO:0070373	negative regulation of ERK1 and ERK2 cascade	Any process that stops, prevents, or reduces the frequency, rate or extent of signal transduction mediated by the ERK1 and ERK2 cascade.
	GO:2000146	negative regulation of cell motility	Any process that stops, prevents, or reduces the frequency, rate or extent of cell motility.
	GO:0043524	negative regulation of neuron apoptotic process	Any process that stops, prevents, or reduces the frequency, rate or extent of cell death by apoptotic process in neurons.
	GO:0032091	negative regulation of protein binding	Any process that stops, prevents, or reduces the frequency, rate or extent of protein binding.
	GO:0042177	negative regulation of protein catabolic process	Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways resulting in the breakdown of a protein by the destruction of the native, active configuration, with or without the hydrolysis of peptide bonds.
	GO:0030512	negative regulation of transforming growth factor beta receptor signaling pathway	Any process that stops, prevents, or reduces the frequency, rate or extent of any TGF-beta receptor signaling pathway.
	GO:0032480	negative regulation of type I interferon production	Any process that stops, prevents, or reduces the frequency, rate, or extent of type I interferon production. Type I interferons include the interferon-alpha, beta, delta, episilon, zeta, kappa, tau, and omega gene families.
	GO:0030182	neuron differentiation	The process in which a relatively unspecialized cell acquires specialized features of a neuron.
	GO:0043547	positive regulation of GTPase activity	Any process that activates or increases the activity of a GTPase.
	GO:0090263	positive regulation of canonical Wnt signaling pathway	Any process that increases the rate, frequency, or extent of the Wnt signaling pathway through beta-catenin, the series of molecular signals initiated by binding of a Wnt protein to a frizzled family receptor on the surface of the target cell, followed by propagation of the signal via beta-catenin, and ending with a change in transcription of target genes.
	GO:0061051	positive regulation of cell growth involved in cardiac muscle cell development	Any process that increases the rate, frequency, or extent of the growth of a cardiac muscle cell, where growth contributes to the progression of the cell over time from its initial formation to its mature state.
	GO:0043525	positive regulation of neuron apoptotic process	Any process that activates or increases the frequency, rate or extent of cell death of neurons by apoptotic process.
	GO:0035307	positive regulation of protein dephosphorylation	Any process that activates or increases the frequency, rate or extent of removal of phosphate groups from a protein.
	GO:0001934	positive regulation of protein phosphorylation	Any process that activates or increases the frequency, rate or extent of addition of phosphate groups to amino acids within a protein.
	GO:0045944	positive regulation of transcription from RNA polymerase II promoter	Any process that activates or increases the frequency, rate or extent of transcription from an RNA polymerase II promoter.
	GO:0051443	positive regulation of ubiquitin-protein transferase activity	Any process that activates, maintains or increases the rate of ubiquitin transferase activity.
	GO:0000413	protein peptidyl-prolyl isomerization	The modification of a protein by cis-trans isomerization of a proline residue.
	GO:0050821	protein stabilization	Any process involved in maintaining the structure and integrity of a protein and preventing it from degradation or aggregation.
	GO:0032465	regulation of cytokinesis	Any process that modulates the frequency, rate or extent of the division of the cytoplasm of a cell and its separation into two daughter cells.
	GO:0007088	regulation of mitotic nuclear division	Any process that modulates the frequency, rate or extent of mitosis.
	GO:0060393	regulation of pathway-restricted SMAD protein phosphorylation	Any process that modulates the rate, frequency or extent of pathway-restricted SMAD protein phosphorylation. Pathway-restricted SMAD proteins and common-partner SMAD proteins are involved in the transforming growth factor beta receptor signaling pathways.
	GO:1900180	regulation of protein localization to nucleus	Any process that modulates the frequency, rate or extent of protein localization to nucleus.
	GO:1901796	regulation of signal transduction by p53 class mediator	Any process that modulates the frequency, rate or extent of signal transduction by p53 class mediator.
	GO:0050808	synapse organization	A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of a synapse, the junction between a neuron and a target (neuron, muscle, or secretory cell).
cellular component
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
	GO:0005829	cytosol	The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
	GO:0030496	midbody	A thin cytoplasmic bridge formed between daughter cells at the end of cytokinesis. The midbody forms where the contractile ring constricts, and may persist for some time before finally breaking to complete cytokinesis.
	GO:0005739	mitochondrion	A semiautonomous, self replicating organelle that occurs in varying numbers, shapes, and sizes in the cytoplasm of virtually all eukaryotic cells. It is notably the site of tissue respiration.
	GO:0043005	neuron projection	A prolongation or process extending from a nerve cell, e.g. an axon or dendrite.
	GO:0016607	nuclear speck	A discrete extra-nucleolar subnuclear domain, 20-50 in number, in which splicing factors are seen to be localized by immunofluorescence microscopy.
	GO:0005654	nucleoplasm	That part of the nuclear content other than the chromosomes or the nucleolus.
	GO:0005634	nucleus	A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.

Asymmetric/Biological Unit
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	PIN1_HUMAN \| Q13526
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