1DM2

HUMAN CYCLIN-DEPENDENT KINASE 2 COMPLEXED WITH THE INHIBITOR HYMENIALDISINE

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Functional Information from GO Data

ChainGOidnamespacecontents
A0015030cellular_componentCajal body
A0005813cellular_componentcentrosome
A0000781cellular_componentchromosome, telomeric region
A0000793cellular_componentcondensed chromosome
A0097123cellular_componentcyclin A1-CDK2 complex
A0097124cellular_componentcyclin A2-CDK2 complex
A0097134cellular_componentcyclin E1-CDK2 complex
A0097135cellular_componentcyclin E2-CDK2 complex
A0000307cellular_componentcyclin-dependent protein kinase holoenzyme complex
A0005737cellular_componentcytoplasm
A0005829cellular_componentcytosol
A0005768cellular_componentendosome
A0005654cellular_componentnucleoplasm
A0005634cellular_componentnucleus
A0005667cellular_componenttranscription factor complex
A0000805cellular_componentX chromosome
A0000806cellular_componentY chromosome
A0005524molecular_functionATP binding
A0030332molecular_functioncyclin binding
A0097472molecular_functioncyclin-dependent protein kinase activity
A0004693molecular_functioncyclin-dependent protein serine/threonine kinase activity
A0000287molecular_functionmagnesium ion binding
A0019904molecular_functionprotein domain specific binding
A0004674molecular_functionprotein serine/threonine kinase activity
A0031145biological_processanaphase-promoting complex-dependent catabolic process
A0051301biological_processcell division
A0071732biological_processcellular response to nitric oxide
A0007099biological_processcentriole replication
A0051298biological_processcentrosome duplication
A0006977biological_processDNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest
A0006281biological_processDNA repair
A0006260biological_processDNA replication
A0000082biological_processG1/S transition of mitotic cell cycle
A0000086biological_processG2/M transition of mitotic cell cycle
A0016572biological_processhistone phosphorylation
A0051321biological_processmeiotic cell cycle
A0031571biological_processmitotic G1 DNA damage checkpoint
A0000122biological_processnegative regulation of transcription by RNA polymerase II
A0018105biological_processpeptidyl-serine phosphorylation
A0008284biological_processpositive regulation of cell proliferation
A0032298biological_processpositive regulation of DNA-dependent DNA replication initiation
A0045893biological_processpositive regulation of transcription, DNA-templated
A0006813biological_processpotassium ion transport
A0006468biological_processprotein phosphorylation
A0007265biological_processRas protein signal transduction
A0010389biological_processregulation of G2/M transition of mitotic cell cycle
A0060968biological_processregulation of gene silencing
A1901796biological_processregulation of signal transduction by p53 class mediator
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Functional Information from PDB Data

site_idNumber of ResiduesDetails
AC112BINDING SITE FOR RESIDUE HMD A 400
ChainResidue
AGLY13
AALA31
AVAL64
APHE80
AGLU81
APHE82
ALEU83
AASN132
ALEU134
AASP145
AHOH566
AHOH580

AC26BINDING SITE FOR RESIDUE EDO A 401
ChainResidue
ALYS88
APRO130
ATRP167
ATYR168
AGLU195
AHOH584

AC35BINDING SITE FOR RESIDUE EDO A 402
ChainResidue
AMET91
AASP92
AGLU195
AARG199
AHOH573

AC45BINDING SITE FOR RESIDUE EDO A 403
ChainResidue
AASN136
ATHR137
AGLU257
ASER261
AHOH539

AC56BINDING SITE FOR RESIDUE EDO A 404
ChainResidue
ATHR137
AGLN265
AHIS268
APRO294
AHIS295
ALEU296

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Functional Information from PDB atom coordinates for the "HETATM" binding sites

site_idNumber of ResiduesDetails
HMD_1dm2_A_400204-(5-AMINO-4-OXO-4H-PYRAZOL-3-YL)-2-BROMO-4,5,6,7-TETRAHYDRO-3AH-PYRROLO[2,3-C]AZEPIN-8-ONE binding site
ChainResidueligand
AILE10HMD: 4-(5-AMINO-4-OXO-4H-PYRAZOL-3-YL)-2-BROMO-4,5,6,7-TETRAHYDRO-3AH-PYRROLO[2,3-C]AZEPIN-8-ONE
AGLU12-THR14HMD: 4-(5-AMINO-4-OXO-4H-PYRAZOL-3-YL)-2-BROMO-4,5,6,7-TETRAHYDRO-3AH-PYRROLO[2,3-C]AZEPIN-8-ONE
AVAL18HMD: 4-(5-AMINO-4-OXO-4H-PYRAZOL-3-YL)-2-BROMO-4,5,6,7-TETRAHYDRO-3AH-PYRROLO[2,3-C]AZEPIN-8-ONE
AALA31HMD: 4-(5-AMINO-4-OXO-4H-PYRAZOL-3-YL)-2-BROMO-4,5,6,7-TETRAHYDRO-3AH-PYRROLO[2,3-C]AZEPIN-8-ONE
ALYS33HMD: 4-(5-AMINO-4-OXO-4H-PYRAZOL-3-YL)-2-BROMO-4,5,6,7-TETRAHYDRO-3AH-PYRROLO[2,3-C]AZEPIN-8-ONE
AVAL64HMD: 4-(5-AMINO-4-OXO-4H-PYRAZOL-3-YL)-2-BROMO-4,5,6,7-TETRAHYDRO-3AH-PYRROLO[2,3-C]AZEPIN-8-ONE
APHE80-ASP86HMD: 4-(5-AMINO-4-OXO-4H-PYRAZOL-3-YL)-2-BROMO-4,5,6,7-TETRAHYDRO-3AH-PYRROLO[2,3-C]AZEPIN-8-ONE
AGLN131-ASN132HMD: 4-(5-AMINO-4-OXO-4H-PYRAZOL-3-YL)-2-BROMO-4,5,6,7-TETRAHYDRO-3AH-PYRROLO[2,3-C]AZEPIN-8-ONE
ALEU134HMD: 4-(5-AMINO-4-OXO-4H-PYRAZOL-3-YL)-2-BROMO-4,5,6,7-TETRAHYDRO-3AH-PYRROLO[2,3-C]AZEPIN-8-ONE
AALA144-ASP145HMD: 4-(5-AMINO-4-OXO-4H-PYRAZOL-3-YL)-2-BROMO-4,5,6,7-TETRAHYDRO-3AH-PYRROLO[2,3-C]AZEPIN-8-ONE

EDO_1dm2_A_40181,2-ETHANEDIOL binding site
ChainResidueligand
ALYS88EDO: 1,2-ETHANEDIOL
AMET91EDO: 1,2-ETHANEDIOL
APRO130-GLN131EDO: 1,2-ETHANEDIOL
ATRP167-TYR168EDO: 1,2-ETHANEDIOL
AGLU195EDO: 1,2-ETHANEDIOL
AALA201EDO: 1,2-ETHANEDIOL

EDO_1dm2_A_40281,2-ETHANEDIOL binding site
ChainResidueligand
ALYS88EDO: 1,2-ETHANEDIOL
AMET91-ASP92EDO: 1,2-ETHANEDIOL
AALA95EDO: 1,2-ETHANEDIOL
AGLU195EDO: 1,2-ETHANEDIOL
AARG199-ALA201EDO: 1,2-ETHANEDIOL

EDO_1dm2_A_40471,2-ETHANEDIOL binding site
ChainResidueligand
AASN136-GLU138EDO: 1,2-ETHANEDIOL
AVAL293-LEU296EDO: 1,2-ETHANEDIOL

EDO_1dm2_A_40341,2-ETHANEDIOL binding site
ChainResidueligand
AGLU257EDO: 1,2-ETHANEDIOL
AARG260-SER261EDO: 1,2-ETHANEDIOL
ASER264EDO: 1,2-ETHANEDIOL

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Functional Information from PROSITE/UniProt

site_idNumber of ResiduesDetails
PS0010813Serine/Threonine protein kinases active-site signature. [LIVMFYC]-x-[HY]-x-D-[LIVMFY]-K-x(2)-N-[LIVMFYCT](3)
ChainResidueDetails
AVAL123-ILE135

PS0010724Protein kinases ATP-binding region signature. [LIV]-G-{P}-G-{P}-[FYWMGSTNH]-[SGA]-{PW}-[LIVCAT]-{PD}-x-[GSTACLIVMFY]
ChainResidueDetails
AILE10-LYS33

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Functional Information from SwissProt/UniProt

site_idNumber of ResiduesDetails
SWS_FT_FI11Proton acceptor.
ChainResidueDetails
AASP127

SWS_FT_FI22Magnesium. {ECO:0000269|PubMed:21565702}
ChainResidueDetails
AASN132
AASP145

SWS_FT_FI33ATP. {ECO:0000255|PROSITE- ProRule:PRU00159, ECO:0000269|PubMed:17095507, ECO:0000269|PubMed:21565702}.
ChainResidueDetails
ALYS33
AASP86
AASP145

SWS_FT_FI44CDK7 binding.
ChainResidueDetails
ALYS9
ALYS88-LYS89
ALEU166

SWS_FT_FI516ATP. {ECO:0000255|PROSITE- ProRule:PRU00159, ECO:0000269|PubMed:17095507, ECO:0000269|PubMed:21565702}.
ChainResidueDetails
AILE10-VAL18
AGLU81-LEU83
ALYS129-ASN132

extCATRES12Mapped from 2phk to 1dm2 using BLAST. All catalytic residues present. Original details record follows: a catalytic site defined by CATRES, Medline 98031892
ChainResidueDetails
AASP149acid/base, activates substrate. removes proton from substrate, which then goes on to attack phosphate group of ATP
ALYS151transition-state stabilisation. stabilises pentavalent phosphate intermediate

CSA12Annotated By Reference To The Literature 1ir3
ChainResidueDetails
AGLN131
AASP127

CSA22Annotated By Reference To The Literature 1ir3
ChainResidueDetails
AASP127
ALYS129

CSA33Annotated By Reference To The Literature 1ir3
ChainResidueDetails
AASP127
ALYS129
ATHR165

CSA43Annotated By Reference To The Literature 1ir3
ChainResidueDetails
AASP127
ALYS129
AASN132

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Catalytic Information from CSA

site_idNumber of ResiduesDetails
CSA12Annotated By Reference To The Literature 1ir3
ChainResidueDetails
AGLN131
AASP127

CSA22Annotated By Reference To The Literature 1ir3
ChainResidueDetails
AASP127
ALYS129

CSA33Annotated By Reference To The Literature 1ir3
ChainResidueDetails
AASP127
ALYS129
ATHR165

CSA43Annotated By Reference To The Literature 1ir3
ChainResidueDetails
AASP127
ALYS129
AASN132