5KQ5 - JenaLib

Asym./Biol. Unit (Jmol Viewer)

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

Title :   AMPK BOUND TO ALLOSTERIC ACTIVATOR

Authors :   M. F. Calabrese, R. G. Kurumbail

Date :   05 Jul 16 (Deposition) - 17 Aug 16 (Release) - 21 Sep 16 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   3.41

Chains :   Asym./Biol. Unit : A,B,C

Keywords :   Kinase Allosteric Activator, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   K. O. Cameron, D. W. Kung, A. S. Kalgutkar, R. G. Kurumbail, R. Miller, C. T. Salatto, J. Ward, J. M. Withka, S. K. Bhattacharya, M. Boehm, K. A. Borzilleri, J. A. Brown, M. Calabrese, N. L. Caspers, E. Cokorinos, E. L. Conn, M. S. Dowling, D. J. Edmonds, H. Eng, D. P. Fernando, R. Frisbie, D. Hepworth, J. Landro, Y. Mao, F. Rajamohan, A. R. Reyes, C. R. Rose, T. Ryder, A. Shavnya, A. C. Smith, M. Tu, A. C. Wolford, J. Xiao
Discovery And Preclinical Characterization Of 6-Chloro-5-[4-(1-Hydroxycyclobutyl) Phenyl]-1H-Indole-3-Carboxylic Acid (Pf-06409577), A Direct Activator Of Adenosine Monophosphate-Activated Protein Kinase (Ampk), For The Potential Treatment Of Diabetic Nephropathy.
J. Med. Chem. V. 59 8068 2016
PubMed-ID: 27490827 | Reference-DOI: 10.1021/ACS.JMEDCHEM.6B00866

Molecule 1 - 5'-AMP-ACTIVATED PROTEIN KINASE CATALYTIC SUBUNIT ALPHA-1
	Chains	:	A
	EC Number	:	2.7.11.1, 2.7.11.27, 2.7.11.31, 2.7.11.26
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Gene	:	PRKAA1, AMPK1
	Organism Common	:	RAT
	Organism Scientific	:	RATTUS NORVEGICUS
	Organism Taxid	:	10116
	Synonym	:	AMPK SUBUNIT ALPHA-1,ACETYL-COA CARBOXYLASE KINASE,ACACA KINASE,HYDROXYMETHYLGLUTARYL-COA REDUCTASE KINASE,HMGCR KINASE,TAU- PROTEIN KINASE PRKAA1

Molecule 2 - 5'-AMP-ACTIVATED PROTEIN KINASE SUBUNIT BETA-1
	Chains	:	B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Fragment	:	RESIDUES 68-270
	Gene	:	PRKAB1
	Mutation	:	YES
	Organism Common	:	RAT
	Organism Scientific	:	RATTUS NORVEGICUS
	Organism Taxid	:	10116
	Synonym	:	AMPKB,5'-AMP-ACTIVATED PROTEIN KINASE 40 KDA SUBUNIT

Molecule 3 - 5'-AMP-ACTIVATED PROTEIN KINASE SUBUNIT GAMMA-1
	Chains	:	C
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Gene	:	PRKAG1
	Organism Common	:	RAT
	Organism Scientific	:	RATTUS NORVEGICUS
	Organism Taxid	:	10116
	Synonym	:	AMPKG

		1	2	3
Asymmetric/Biological Unit	:	A	B	C

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (7, 11)

No.	Name	Count	Type	Full Name
1	6VT	1	Ligand/Ion	6-CHLORANYL-5-[4-(1-OXIDANYLCYCLOBUTYL)PHENYL]-1~{H}-INDOLE-3-CARBOXYLIC ACID
2	ADP	1	Ligand/Ion	ADENOSINE-5'-DIPHOSPHATE
3	AMP	2	Ligand/Ion	ADENOSINE MONOPHOSPHATE
4	CL	4	Ligand/Ion	CHLORIDE ION
5	SO4	1	Ligand/Ion	SULFATE ION
6	STU	1	Ligand/Ion	STAUROSPORINE
7	TPO	1	Mod. Amino Acid	PHOSPHOTHREONINE

Asymmetric Unit (9, 9)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	LEU A:22 , GLY A:23 , VAL A:24 , GLY A:25 , VAL A:30 , ALA A:43 , ILE A:77 , MET A:93 , GLU A:94 , TYR A:95 , VAL A:96 , GLY A:99 , GLU A:100 , GLU A:143 , ASN A:144 , LEU A:146 , ALA A:156 , ASP A:157	binding site for residue STU A 601
2	AC2	SOFTWARE	LEU A:18 , GLY A:19 , LYS A:29 , LYS A:31 , ILE A:46 , ASP A:88 , ARG B:83 , THR B:106 , ASP B:108 , VAL B:113	binding site for residue 6VT A 602
3	AC3	SOFTWARE	SER A:97 , ALA A:149	binding site for residue CL A 603
4	AC4	SOFTWARE	VAL A:24	binding site for residue CL A 605
5	AC5	SOFTWARE	LYS A:34 , LYS A:41	binding site for residue CL A 606
6	AC6	SOFTWARE	HIS C:150 , THR C:199 , ILE C:203 , ALA C:204 , VAL C:224 , SER C:225 , ALA C:226 , HIS C:297 , ARG C:298 , ILE C:311 , SER C:313 , SER C:315 , ASP C:316	binding site for residue AMP C 401
7	AC7	SOFTWARE	ARG C:69 , ILE C:239 , SER C:241 , PHE C:243 , ASP C:244 , ARG C:268 , LEU C:276 , VAL C:296 , HIS C:297 , ARG C:298 , SO4 C:404	binding site for residue AMP C 402
8	AC8	SOFTWARE	ARG C:69 , MET C:84 , THR C:86 , ILE C:87 , THR C:88 , ASP C:89 , TYR C:120 , PRO C:127 , LEU C:128 , VAL C:129 , HIS C:150 , ARG C:151 , PRO C:153	binding site for residue ADP C 403
9	AC9	SOFTWARE	ARG C:151 , THR C:167 , AMP C:402	binding site for residue SO4 C 404

(no "SS Bond" information available for 5KQ5)

(no "Cis Peptide Bond" information available for 5KQ5)

(no "SAP(SNP)/Variant" information available for 5KQ5)

(no "PROSITE Motif" information available for 5KQ5)

(no "Exon" information available for 5KQ5)

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
	(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:363
                                                                                                                                                                                                                                                                                                                                                                                                           
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..ee..eeeeeeeee....eeeeeee.....eeeeeeeehhhhhhh.hhhhhhhhhhhhh.........eeeeee...eeeeeee....eehhhhhhhh...hhhhhhhhhhhhhhhhhhhhh..ee........eee.....eee.hhhhhee.................hhhhhh.....hhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhh.........hhhhhhhhhhhh..hhhhh.hhhhhhhhhhhhh.........eee......hhhhhhhhhhhhhhhhh.eeee....eeeeeee......eeeeeeeeee.....eeeeeeee...hhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5kq5 A  10 RVKIGHYILGDTLGVGTFGKVKVGKHELTGHKVAVKILNRQKIRSLDVVGKIRREIQNLKLFRHPHIIKLYQVISTPSDIFMVMEYVSGGELFDYICKNGRLDEKESRRLFQQILSGVDYCHRHMVVHRDLKPENVLLDAHMNAKIADFGLSNMMSDGEFLRtSCGSPNYAAPEVISGRLYAGPEVDIWSSGVILYALLCGTLPFDDDHVPTLFKKICDGIFYTPQYLNPSVISLLKHMLQVDPMKRATIKDIREHEWFKQDLPKYLFAKWHLGIRSQSRPNDIMAEVCRAIKQLDYEWKVVNPYYLRVRRKNPVTSTFSKMSLQLYQVDSRTYLLDFRSIDPGSHTIEFFEMCANLIKILAQ 548
                                    19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169  |    179       189       199       209       219       229       239       249       259       269       395       405       415       425       435       445       455       465 ||    535       545   
                                                                                                                                                                                            172-TPO                                                                                                  277|                                                                      467|                    
                                                                                                                                                                                                                                                                                                      394                                                                       528

Chain B from PDB  Type:PROTEIN  Length:160
                                                                                                                                                                                                
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeee......eeee.hhh...ee.ee...eeeeeee....eeeeeeee..eee......eee.....eeeeee.hhhhhhhhhhhhhhh.......hhhhhh...............hhhhh...eeeeee..eeeeeeeeee..eeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5kq5 B  78 RPTVFRWTGGGKEVYLSGSFNNWSKLPLTRDQNNFVAILDLPEGEHQYKFFVDGQWTHDPSEPIVTSQLGTVNNIIQVKKTDFEVFDALMVDSQKAPPILPPHLLQVILNKSCDPALLPEPNHVMLNHLYALSIKDGVMVLSATHRYKKKYVTTLLYKPI 270
                                    87        97       107       117       127       137       147       157       167   ||  206       216||     230       240       250       260       270
                                                                                                                       171|             217|                                                
                                                                                                                        201              222

Chain C from PDB  Type:PROTEIN  Length:281
                                                                                                                                                                                                                                                                                                                         
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhh..eeeeeeee...hhhhhhhhhhhh...eeeee......eeeeeehhhhhhhhhhhh......hhhhhh.hhhhhhhhhh..............hhhhhhhhhhhhh..eeeee......eeeeeehhhhhhhhhh......hhhhhh.........ee...hhhhhhhhhhhhh..eeeee.....eeeeee...hhhhhhh........hhhhhhhhh.ee....hhhhhhhhhhh....eeeee.....eeeeeehhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5kq5 C  28 YTTFMKSHRCYDLIPTSSKLVVFDTSLQVKKAFFALVTNGVRAAPLWDSKKQSFVGMLTITDFINILHRYYKSALVQIYELEEHKIETWREVYLQDSFKPLVCISPNASLFDAVSSLIRNKIHRLPVIDPESGNTLYILTHKRILKFLKLFITMSKSLEELQIGTYANIAMVRTTTPVYVALGIFVQHRVSALPVVDEKGRVVDIYSKFDVINLAAEKTYNNLDVSVTKALQHRLKCYLHETLEAIINRLVEAEVHRLVVVDEHDVVKGIVSLSDILQALV 322
                                    37        47        57        67        77        87        97       107       117       127       137       147       157       167       177  ||   194       204       214       224       234       244       254       264   ||  281       291       301       311       321 
                                                                                                                                                                                  180|                                                                             268|                                              
                                                                                                                                                                                   188                                                                              276

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	extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '\|'

(no "SCOP Domain" information available for 5KQ5)

(no "CATH Domain" information available for 5KQ5)

(no "Pfam Domain" information available for 5KQ5)

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Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (7, 11)

Sites (9, 9)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

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Gene Ontology (85, 110)

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