4LUE - JenaLib

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Title :   CRYSTAL STRUCTURE OF HCK IN COMPLEX WITH 7-[TRANS-4-(4-METHYLPIPERAZIN-1-YL)CYCLOHEXYL]-5-(4-PHENOXYPHENYL)-7H-PYRROLO[2,3-D]PYRIMIDIN-4-AMINE (RESULTING FROM DISPLACEMENT OF SKF86002)

Authors :   L. J. Parker, A. Tanaka, N. Handa, K. Honda, Y. Tomabechi, M. Shirouzu, S

Date :   25 Jul 13 (Deposition) - 12 Feb 14 (Release) - 12 Feb 14 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   3.04

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

Keywords :   Cocrystallization, Skf86002, Fluorescence, Inhibitor Screening, Kinase, Transferase-Transferase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   L. J. Parker, S. Taruya, K. Tsuganezawa, N. Ogawa, J. Mikuni, K. Honda, T. Tomabechi, N. Handa, M. Shirouzu, S. Yokoyama, A. Tanaka
Kinase Crystal Identification And Atp-Competitive Inhibitor Screening Using The Fluorescent Ligand Skf86002
Acta Crystallogr. , Sect. D V. 70 392 2014
PubMed: search | Reference-DOI: 10.1107/S1399004713028654

Molecule 1 - TYROSINE-PROTEIN KINASE HCK
	Chains	:	A, B
	EC Number	:	2.7.10.2
	Engineered	:	YES
	Expression System	:	SPODOPTERA FRUGIPERDA
	Expression System Taxid	:	7108
	Expression System Vector Type	:	BACULOVIRUS
	Fragment	:	UNP RESIDUES 81-526
	Gene	:	HCK
	Mutation	:	YES
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	HEMATOPOIETIC CELL KINASE, HEMOPOIETIC CELL KINASE, P59- HCK/P60-HCK, P59HCK, P61HCK

		1	2
Asymmetric Unit	:	A	B
Biological Unit 1 (1x)	:	A
Biological Unit 2 (1x)	:		B

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (6, 13)

No.	Name	Count	Type	Full Name
1	CA	2	Ligand/Ion	CALCIUM ION
2	CL	2	Ligand/Ion	CHLORIDE ION
3	GOL	4	Ligand/Ion	GLYCEROL
4	IMD	1	Ligand/Ion	IMIDAZOLE
5	PTR	2	Mod. Amino Acid	O-PHOSPHOTYROSINE
6	VSE	2	Ligand/Ion	7-[TRANS-4-(4-METHYLPIPERAZIN-1-YL)CYCLOHEXYL]-5-(4-PHENOXYPHENYL)-7H-PYRROLO[2,3-D]PYRIMIDIN-4-AMINE

Biological Unit 1 (3, 4)

No.	Name	Count	Type	Full Name
1	CA	-1	Ligand/Ion	CALCIUM ION
2	CL	-1	Ligand/Ion	CHLORIDE ION
3	GOL	2	Ligand/Ion	GLYCEROL
4	IMD	-1	Ligand/Ion	IMIDAZOLE
5	PTR	1	Mod. Amino Acid	O-PHOSPHOTYROSINE
6	VSE	1	Ligand/Ion	7-[TRANS-4-(4-METHYLPIPERAZIN-1-YL)CYCLOHEXYL]-5-(4-PHENOXYPHENYL)-7H-PYRROLO[2,3-D]PYRIMIDIN-4-AMINE

Biological Unit 2 (4, 5)

No.	Name	Count	Type	Full Name
1	CA	-1	Ligand/Ion	CALCIUM ION
2	CL	-1	Ligand/Ion	CHLORIDE ION
3	GOL	2	Ligand/Ion	GLYCEROL
4	IMD	1	Ligand/Ion	IMIDAZOLE
5	PTR	1	Mod. Amino Acid	O-PHOSPHOTYROSINE
6	VSE	1	Ligand/Ion	7-[TRANS-4-(4-METHYLPIPERAZIN-1-YL)CYCLOHEXYL]-5-(4-PHENOXYPHENYL)-7H-PYRROLO[2,3-D]PYRIMIDIN-4-AMINE

Asymmetric Unit (11, 11)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	GLU A:490 , GLU B:524 , PTR B:527	BINDING SITE FOR RESIDUE CA A 601
02	AC2	SOFTWARE	VAL A:281 , ALA A:293 , LYS A:295 , VAL A:323 , THR A:338 , GLU A:339 , MET A:341 , GLY A:344 , SER A:345 , ASP A:348 , ASP A:404 , PHE A:405 , GOL A:605	BINDING SITE FOR RESIDUE VSE A 602
03	AC3	SOFTWARE	ARG A:85 , ARG A:123 , ARG A:128	BINDING SITE FOR RESIDUE CL A 603
04	AC4	SOFTWARE	ARG A:388 , ASN A:391 , ASP A:404 , HOH A:704	BINDING SITE FOR RESIDUE GOL A 604
05	AC5	SOFTWARE	PHE A:340 , MET A:341 , ALA A:342 , GLY A:344 , VSE A:602	BINDING SITE FOR RESIDUE GOL A 605
06	AC6	SOFTWARE	GLU A:524 , PTR A:527 , GLU B:490	BINDING SITE FOR RESIDUE CA B 601
07	AC7	SOFTWARE	ASN B:391 , ASP B:404	BINDING SITE FOR RESIDUE GOL B 602
08	AC8	SOFTWARE	LEU B:273 , VAL B:281 , ALA B:293 , LYS B:295 , VAL B:323 , ILE B:336 , THR B:338 , GLU B:339 , MET B:341 , SER B:345 , ASP B:348 , ASP B:404 , PHE B:405 , GOL B:606	BINDING SITE FOR RESIDUE VSE B 603
09	AC9	SOFTWARE	ARG B:85 , ARG B:123 , ARG B:128	BINDING SITE FOR RESIDUE CL B 604
10	BC1	SOFTWARE	GLU B:145 , GLU B:147 , PHE B:150 , SER B:248	BINDING SITE FOR RESIDUE IMD B 605
11	BC2	SOFTWARE	LEU B:273 , PHE B:340 , MET B:341 , ALA B:342 , GLY B:344 , VSE B:603	BINDING SITE FOR RESIDUE GOL B 606

(no "SS Bond" information available for 4LUE)

Asymmetric Unit

No.	Residues
1	Glu A:332	-	Pro A:333
2	Glu B:332	-	Pro B:333

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

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

(no "Exon" information available for 4LUE)

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:423
                                                                                                                                                                                                                                                                                                                                                                                                                                                                       
               SCOP domains d4luea1 A:85-146 automated matches                            d4luea2 A:147-249 automated matches                                                                d4luea3 A:250-530 Haemopoetic cell kinase Hck                                                                                                                                                                                                                          SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee..................eeeeeee...eeeeee.....eeeee...eee.........ee...hhhhhhhhhh........eeeee.......eeeeeeeee...eeeeeeeee.............hhhhhhhhhhh.............................hhhhh...eeeee...eeeeeeee...eeeeeeee.....hhhhhhh.........eeeee.....eeee......hhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhh.......hhh.eee.....eee...hhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhh.........hhhhhhhhhhh..........hhhhhhhhhhhh..hhhhh.hhhhhhhhhhh...hhhh.ee.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4lue A  85 RIIVVALYDYEAIHHEDLSFQKGDQMVVLEESGEWWKARSLATRKEGYIPSNYVARVDSLETEEWFFKGISRKDAERQLLAPGNMLGSFMIRDSETTKGSYSLSVRDYDPRQGDTVKHYKIRTGFYISPRSTFSTLQELVDHYKKGNDGLCQKLSVPCMSSKPQKPWEKDAWEIPRESLKLEKKLGAGQFGEVWMATYNKHTKVAVKTMKPGSLAEANVMKTLQHDKLVKLHAVVTKEPIYIITEFMAKGSLLDFLKSDEGSKQPLPKLIDFSAQIAEGMAFIEQRNYIHRDLRAANILVSASLVCKIADFGLARVIPIKWTAPEAINFGSFTIKSDVWSFGILLMEIVTYGRIPYPGMSNPEVIRALERGYRMPRPENCPEELYNIMMRCWKNRPEERPTFEYIQSVLDDFYTATESQyEEI 530
                                    94       104       114       124       134       144       154       164       174       184       194       204  ||   218       228       238       248       258       268       278       288       298  ||   314       324       334       344       354       364       374       384       394       404      |427       437       447       457       467       477       487       497       507       517       527   
                                                                                                                                                    207|                                                                                      301|                                                                                                    411|                                                                                                   527-PTR
                                                                                                                                                     212                                                                                       308                                                                                                     425

Chain B from PDB  Type:PROTEIN  Length:418
                                                                                                                                                                                                                                                                                                                                                                                                                                                                  
               SCOP domains d4lueb1 B:85-146 automated matches                            d4lueb2 B:147-249 automated matches                                                                d4lueb3 B:250-530 Haemopoetic cell kinase Hck                                                                                                                                                                                                                     SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee..................eeeeeee...eeeeee.....eeeee...eee.........ee...hhhhhhhhhh........eeeee.......eeeeeeeee...eeeeeeeee.............hhhhhhhhhhh.............................hhhhh...eeeee...eeeeeeee...eeeeeeee...hhhhhhh.........eeeee....eeeee......hhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhh...........eee.....eee...hhhhhhhhhhh.......hhhhhhhhhhhhhhhhhh.........hhhhhhhhhhh..........hhhhhhhhhhhh..hhhhh.hhhhhhhhhhh...hhhhh.... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4lue B  85 RIIVVALYDYEAIHHEDLSFQKGDQMVVLEESGEWWKARSLATRKEGYIPSNYVARVDSLETEEWFFKGISRKDAERQLLAPGNMLGSFMIRDSETTKGSYSLSVRDYDPRQGDTVKHYKIRTGFYISPRSTFSTLQELVDHYKKGNDGLCQKLSVPCMSSKPQKPWEKDAWEIPRESLKLEKKLGAGQFGEVWMATYNKHTKVAVKTMKPLAEANVMKTLQHDKLVKLHAVVTKEPIYIITEFMAKGSLLDFLKSDEGSKQPLPKLIDFSAQIAEGMAFIEQRNYIHRDLRAANILVSASLVCKIADFGLARVIPIKWTAPEAINFTIKSDVWSFGILLMEIVTYGRIPYPGMSNPEVIRALERGYRMPRPENCPEELYNIMMRCWKNRPEERPTFEYIQSVLDDFYTATESQyEEI 530
                                    94       104       114       124       134       144       154       164       174       184       194       204  ||   218       228       238       248       258       268       278       288       298||     316       326       336       346       356       366       376       386       396       406    || 429     ||442       452       462       472       482       492       502       512       522    |   
                                                                                                                                                    207|                                                                                    299|                                                                                                    411|       435|                                                                                     527-PTR
                                                                                                                                                     212                                                                                     308                                                                                                     425        439

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	-	→ Gap	(green background, '-', border residues have a numbering label)
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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 '\|'

Asymmetric Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: All beta proteins (24004)

Fold: SH3-like barrel (1035)

Superfamily: SH3-domain (369)

Family: automated matches (114)

Protein domain: automated matches (114)

Human (Homo sapiens) [TaxId: 9606] (74)

1a	d4luea1	A:85-146
1b	d4lueb1	B:85-146

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

Fold: Protein kinase-like (PK-like) (2589)

Superfamily: Protein kinase-like (PK-like) (2589)

Family: Protein kinases, catalytic subunit (1977)

Protein domain: Haemopoetic cell kinase Hck (19)

Human (Homo sapiens) [TaxId: 9606] (19)

2a	d4luea3	A:250-530
2b	d4lueb3	B:250-530

Fold: SH2-like (260)

Superfamily: SH2 domain (260)

Family: automated matches (35)

Protein domain: automated matches (35)

Human (Homo sapiens) [TaxId: 9606] (30)

3a	d4luea2	A:147-249
3b	d4lueb2	B:147-249

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

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

Asymmetric Unit(hide GO term definitions)

Asymmetric Unit
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	Cis Peptide Bonds
		Glu A:332 - Pro A:333	[ RasMol ]
		Glu B:332 - Pro B:333	[ RasMol ]

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	4lue
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4ll5	CRYSTAL STRUCTURE OF PIM1 IN COMPLEX WITH THE FLUORESCENT COMPOUND SKF86002
4lm5	CRYSTAL STRUCTURE OF PIM1 IN COMPLEX WITH 2-{4-[(3- AMINOPROPYL) AMINO]QUINAZOLIN-2-YL}PHENOL (RESULTING FROM DISPLACEMENT OF SKF86002)
4lmu	CRYSTAL STRUCTURE OF PIM1 IN COMPLEX WITH THE INHIBITOR QUERCETIN (RESULTING FROM DISPLACEMENT OF SKF86002)
4lud	CRYSTAL STRUCTURE OF HCK IN COMPLEX WITH THE FLUORESCENT COMPOUND SKF86002

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (6, 13)

Sites (11, 11)

SS Bonds (0, 0)

Cis Peptide Bonds (2, 2)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (0, 0)

Sequences/Alignments

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SCOP Domains (3, 6)

CATH Domains (0, 0)

Pfam Domains (0, 0)

Gene Ontology (59, 59)

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