Structure of PDB 7sic Chain A Binding Site BS01

Receptor Information
>7sic Chain A (length=2773) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
LNDLLICCRQLEHDRATERKKEVEKFKRLIRDPETIKHLDNWDAVFRFLQ
KYIQKETECQASRQKKMQEISSLVKYFIKCANRRAPRLKCQELLNYIMDT
VKDSSNGAIYGADCSNILLKDILSVRKYWCEISQQQWLELFSVYFRLYLK
PSQDVHRVLVARIIHAVTKGCCSQTDGLNSKFLDFFSKAIQCARQEKSSS
GLNHILAALTIFLKTLAVNFRIRVCELGDEILPTLLYIWTQHRLNDSLKE
VIIELFQLQIYIHHPKGAKTQEKGAYESTKWRSILYNLYDLLVNEISHIG
SRRNIAVKENLIELMADICHQVFNIELGWEVIKDHLQKSQNDFDLVPWLQ
IATQLISKYPASLPNCELSPLLMILSQLLPQQRHGERTPYVLRCLTEVAL
CQDKRSNLESSQKSDLLKLWNKIWCITFRGISSEQIQAENFGLLGAIIQG
SLVEVDREFWKLFTGSACRPSCPAVCCLTLALTTSIVPGTFSLKESIMKW
LLFYQLETEVPPILHSNFPHLVLEKILVSLTMKNCKAAMNFFQSVPECSF
SEVEELFLQTTFDKMDFLTGFSVHQNLKESLDRCLLGLSEQLLNNYSSEI
TNSETLVRCSRLLVGVLGCYCYMGVIAEEEAYKSELFQKAKSLMQCAGES
ITLFKNKTNEEFRIGSLRNMMQLCTRCLSNCTKKSPNKIASGFFLRLLTS
KLMNDIADICKSLASFISTIGAINPLAEEYLSKQDLLFLDMLKFLCLCVT
TAQTNTVSFRAADIRRKLLMLIDSSTLEPTKSLHLHMYLMLLKELPGEEY
PLPMEDVLELLKPLSNVCSLYRRDQDVCKTILNHVLHVVKNLGQSNMDSE
NTRDAQGQFLTVIGAFWHLTKERKYIFSVRMALVNCLKTLLEADPYSKWA
ILNVMGKDFPVNEVFTQFLADNHHQVRMLAAESINRLFQDTKLKALPLKL
QQTAFENAYLKAQEGMREMETLDEIYNRKSVLLTLIAVVLSCSPICEKQA
LFALCKSVKENGLEPHLVKKVLEKVSETFGYRRLEDFMASHLDYLVLEWL
NLQDTEYNLSSFPFILLNYTNIEDFYRSCYKVLIPHLVIRSHFDEVKSIA
NQIQEDWKSLLTDCFPKILVNILPYFAYEGTRDSGMAQQRETATKVYDML
KSENLLGKQIDHLFISNLPEIVVELLMTLHEPDLDPAPNPPHFPSHVIKA
TFAYISNCHKTKLKSILEILSKSPDSYQKILLAICEQAAETNNVYKKHRI
LKIYHLFVSLLLKDIKSGLGGAWAFVLRDVIYTLIHYINQRPSCIMDVSL
RSFSLCCDLLSQVCQTAVTYCKDALENHLHVIVGTLIPLVYEQVEVQKQV
LDLLKYLVIDNKDNENLYITIKLLDPFPDHVVFKDLRITQQKIKYSRGPF
SLLEEINHFLSVSVYDALPLTRLEGLKDLRRQLELHKDQMVDIMRASQDN
PQDGIMVKLVVNLLQLSKMAINHTGEKEVLEAVGSCLGEVGPIDFSTIAI
QHSKDASYTKALKLFEDKELQWTFIMLTYLNNTLVEDCVKVRSAAVTCLK
NILATKTGHSFWEIYKMTTDPMLAYLQPFRTSRKKFLEVPRFDKENPFEG
LDDINLWIPLSENHDIWIKTLTCAFLDSGGTKCEILQLLKPMCEVKTDFC
QTVLPYLIHDILLQDTNESWRNLLSTHVQGFFTSCLRHCCLDKKSQRTML
AVVDYMRRQKRPSSGTIFNDAFWLDLNYLEVAKVAQSCAAHFTALLYAEI
YADKKSMDDQEKRSTTISSLSEKSKEETGISLQDLLLEIYRSIGEPDSLY
GCGGGKMLQPITRLRTYEHEAMWGKALVTYDLETAIPSSTRQAGIIQALQ
NLGLCHILSVYLKGLDYENKDWCPELEELHYQAAWRNMQWDHCGTSYHES
LYNALQSLRDREFSTFYESLKYARVKEVEEMCKRSLESVYSLYPTLSRLQ
AIGELESIGELFSRSVTHRQLSEVYIKWQKHSQLLKDSDFSFQEPIMALR
TVILEILMEKEMDNSQRECIKDILTKHLVELSILARTFKNTQLPERAIFQ
IKQYNSVSCGVSEWQLEEAQVFWAKKEQSLALSILKQMIKKLDASCAANN
PSLKLTYTECLRVCGNWLAETCLENPAVIMQTYLEKAVEVAGNYDGESSD
ELRNGKMKAFLSLARFSDTQYQRIENYMKSSEFENKQALLKRAKERYTVK
VQRELELDELALRALKEDRKRFLCKAVENYINCLLSGEEHDMWVFRLCSL
WLENSGVSEVNGMMKRDGMKIPTYKFLPLMYQLAARMGTKMMGGLGFHEV
LNNLISRISMDHPHHTLFIILALANANRDEFLTSSQLDEDRTEAANRIIC
TIRSRRPQMVRSVEALCDAYIILANLDATQWKTQRKGINIPADQPITKLK
NLEDVVVPTMEIKVDHTGEYGNLVTIQSFKAEFRLAGGVNLPKIIDCVGS
DGKERRQLVKGRDDLRQDAVMQQVFQMCNTLLQRNTETRKRKLTICTYKV
VPLSQRSGVLEWCTGTVPIGEFLVNNEDGAHKRYRPNDFSAFQCQKKMME
VQKKSFEEKYEVFMDVCQNFQPVFRYFCMEKFLDPAIWFEKRLAYTRSVA
TSSIVGYILGLGDRHVQNILINEQSAELVHIDLGVAFEQGKILPTPETVP
FRLTRDIVDGMGITGVEGVFRRCCEKTMEVMRNSQETLLTIVEVLLYDPL
FDWTMNPLKALYLQQRPSFNKVAERVLMRLQEKLKGVEEGTVLSVGGQVN
LLIQQAIDPKNLSRLFPGWKAWV
Ligand information
Ligand IDANP
InChIInChI=1S/C10H17N6O12P3/c11-8-5-9(13-2-12-8)16(3-14-5)10-7(18)6(17)4(27-10)1-26-31(24,25)28-30(22,23)15-29(19,20)21/h2-4,6-7,10,17-18H,1H2,(H,24,25)(H2,11,12,13)(H4,15,19,20,21,22,23)/t4-,6-,7-,10-/m1/s1
InChIKeyPVKSNHVPLWYQGJ-KQYNXXCUSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.7.0c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(O)OP(=O)(NP(=O)(O)O)O)O)O)N
CACTVS 3.370Nc1ncnc2n(cnc12)[CH]3O[CH](CO[P](O)(=O)O[P](O)(=O)N[P](O)(O)=O)[CH](O)[CH]3O
CACTVS 3.370Nc1ncnc2n(cnc12)[C@@H]3O[C@H](CO[P](O)(=O)O[P](O)(=O)N[P](O)(O)=O)[C@@H](O)[C@H]3O
ACDLabs 12.01O=P(O)(O)NP(=O)(O)OP(=O)(O)OCC3OC(n2cnc1c(ncnc12)N)C(O)C3O
OpenEye OEToolkits 1.7.0c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)CO[P@](=O)(O)O[P@@](=O)(NP(=O)(O)O)O)O)O)N
FormulaC10 H17 N6 O12 P3
NamePHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
ChEMBLCHEMBL1230989
DrugBank
ZINCZINC000008660410
PDB chain7sic Chain A Residue 3101 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

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PDB7sic Structure of the human ATM kinase and mechanism of Nbs1 binding.
Resolution2.51 Å
Binding residue
(original residue number in PDB)		K2717 W2769 C2770 Q2874 I2888 D2889 Y2969
Binding residue
(residue number reindexed from 1)		K2460 W2512 C2513 Q2617 I2631 D2632 Y2712
Annotation score3
Enzymatic activity
Enzyme Commision number 2.7.11.1: non-specific serine/threonine protein kinase.
Gene Ontology
Molecular Function
GO:0003677 DNA binding
GO:0004672 protein kinase activity
GO:0004674 protein serine/threonine kinase activity
GO:0004677 DNA-dependent protein kinase activity
GO:0005515 protein binding
GO:0005524 ATP binding
GO:0016301 kinase activity
GO:0016303 1-phosphatidylinositol-3-kinase activity
GO:0035979 histone H2AXS139 kinase activity
GO:0042802 identical protein binding
GO:0044024 histone H2AS1 kinase activity
GO:0044877 protein-containing complex binding
GO:0106310 protein serine kinase activity
Biological Process
GO:0000077 DNA damage checkpoint signaling
GO:0000425 pexophagy
GO:0000723 telomere maintenance
GO:0000724 double-strand break repair via homologous recombination
GO:0000729 DNA double-strand break processing
GO:0001541 ovarian follicle development
GO:0001666 response to hypoxia
GO:0001756 somitogenesis
GO:0002331 pre-B cell allelic exclusion
GO:0002376 immune system process
GO:0006281 DNA repair
GO:0006302 double-strand break repair
GO:0006303 double-strand break repair via nonhomologous end joining
GO:0006338 chromatin remodeling
GO:0006468 protein phosphorylation
GO:0006974 DNA damage response
GO:0006977 DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest
GO:0007094 mitotic spindle assembly checkpoint signaling
GO:0007095 mitotic G2 DNA damage checkpoint signaling
GO:0007131 reciprocal meiotic recombination
GO:0007140 male meiotic nuclear division
GO:0007143 female meiotic nuclear division
GO:0007165 signal transduction
GO:0007292 female gamete generation
GO:0007420 brain development
GO:0007507 heart development
GO:0008340 determination of adult lifespan
GO:0008585 female gonad development
GO:0008630 intrinsic apoptotic signaling pathway in response to DNA damage
GO:0009791 post-embryonic development
GO:0010212 response to ionizing radiation
GO:0010506 regulation of autophagy
GO:0010628 positive regulation of gene expression
GO:0016310 phosphorylation
GO:0018105 peptidyl-serine phosphorylation
GO:0030335 positive regulation of cell migration
GO:0030889 negative regulation of B cell proliferation
GO:0032210 regulation of telomere maintenance via telomerase
GO:0032212 positive regulation of telomere maintenance via telomerase
GO:0033151 V(D)J recombination
GO:0033554 cellular response to stress
GO:0034614 cellular response to reactive oxygen species
GO:0035264 multicellular organism growth
GO:0036092 phosphatidylinositol-3-phosphate biosynthetic process
GO:0036289 peptidyl-serine autophosphorylation
GO:0042159 lipoprotein catabolic process
GO:0042770 signal transduction in response to DNA damage
GO:0042981 regulation of apoptotic process
GO:0043065 positive regulation of apoptotic process
GO:0043517 positive regulation of DNA damage response, signal transduction by p53 class mediator
GO:0043525 positive regulation of neuron apoptotic process
GO:0045141 meiotic telomere clustering
GO:0045785 positive regulation of cell adhesion
GO:0045944 positive regulation of transcription by RNA polymerase II
GO:0046777 protein autophosphorylation
GO:0048538 thymus development
GO:0048599 oocyte development
GO:0051402 neuron apoptotic process
GO:0051726 regulation of cell cycle
GO:0070192 chromosome organization involved in meiotic cell cycle
GO:0071044 histone mRNA catabolic process
GO:0071300 cellular response to retinoic acid
GO:0071479 cellular response to ionizing radiation
GO:0071480 cellular response to gamma radiation
GO:0071481 cellular response to X-ray
GO:0071500 cellular response to nitrosative stress
GO:0080090 regulation of primary metabolic process
GO:0080135 regulation of cellular response to stress
GO:0090398 cellular senescence
GO:0090399 replicative senescence
GO:0097694 establishment of RNA localization to telomere
GO:0097695 establishment of protein-containing complex localization to telomere
GO:1900034 regulation of cellular response to heat
GO:1901796 regulation of signal transduction by p53 class mediator
GO:1903626 positive regulation of DNA catabolic process
GO:1903978 regulation of microglial cell activation
GO:1904262 negative regulation of TORC1 signaling
GO:1904354 negative regulation of telomere capping
GO:1904358 positive regulation of telomere maintenance via telomere lengthening
GO:1904884 positive regulation of telomerase catalytic core complex assembly
GO:2000785 regulation of autophagosome assembly
Cellular Component
GO:0000781 chromosome, telomeric region
GO:0005634 nucleus
GO:0005654 nucleoplasm
GO:0005730 nucleolus
GO:0005737 cytoplasm
GO:0005777 peroxisome
GO:0005782 peroxisomal matrix
GO:0005813 centrosome
GO:0005819 spindle
GO:0005829 cytosol
GO:0005856 cytoskeleton
GO:0031410 cytoplasmic vesicle
GO:0035861 site of double-strand break
GO:0043231 intracellular membrane-bounded organelle
GO:0098850 extrinsic component of synaptic vesicle membrane
GO:1990391 DNA repair complex

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:7sic, PDBe:7sic, PDBj:7sic
PDBsum7sic
PubMed35076389
UniProtQ13315|ATM_HUMAN Serine-protein kinase ATM (Gene Name=ATM)

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