Structure of PDB 6z2x Chain F Binding Site BS01

Receptor Information
>6z2x Chain F (length=2325) Species: 559292 (Saccharomyces cerevisiae S288C) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
ESHVKYLDELILAIKDLNSGVDSKVQIKKVPSLKILNTLIRNLKDQRRNN
IMKNDTIFSKTVSALALLLEYNPFLLVMKDSNGNFEIQRLIDDFLNISVL
NYDNYHRIWFMRRKLGSWCKACVEFYGKPAKFQLTAHFENTMNLYEQALT
EVLLGKTELLKFYDTLKGLYILLYWFTSEYSTFGNSIAFLDSSLGFTKFD
FNFQRLIRIVLYVFDSCELAALEYAEIQLKYISLVVDYVCNRTISTALDA
PALVCCEQLKFVLTTMHHFLDNKYGLLDNDPTMAKGILRLYSLCISNDFS
KCFVDHFPIDQWADFSQSEHFPFTQLTNKALSIVYFDLKRRSLPVEALKY
DNKFNIWVYQSEPDSSLKNVTSPFDDRYKQLEKLRLLVLKKFNKTERGTL
LKYRVNQLSPGFFQRAGNDFKLILNEASVSIQTCFKTNNITRLTSWTVIL
GRLACLESEKFSSTKDMDNWYVCHLCDIEKTGNPFVRINPNRPEAAGKSE
IFRILHSNFLSHPNIDEFSESLLSGILFSLHRIFSHFQPPKLTDGNGQIN
KSFKLVQKCFMNSNRYLRLLSTRIIPLFNISDSHNSEDEHTATLIKFLQS
QKLPVVKENLVIAWTQLTLTTSNDVFDTLLLKLIDIFNSDDYSLRIMMTL
QIKNMAKILKKTPYQLLSPILPVLLRQLGKNLVERKVGFQNLIELLGYSS
KTILDIFQRYIIPYAIIQYKSDVLSEIAKIMCDGDTSLINQMKVNLLKKN
SRQIFAVALVKHGLFSLDILETLFLNRAPTFDKGYITAYLPDYKTLAEIT
KLYKNSVTKDASDSENANMILCSLRFLITNFEKDKRHGSKYKNINNWTDD
QEQAFQKKLQDNILGIFQVFSSDIHDVEGRTTYYEKLRVINGISFLIIYA
PKKSIISALAQISICLQTGLGLKEVRYEAFRCWHLLVRHLNDEELSTVID
SLIAFILQKWSEFNGKLRNIVYSILDTLIKEKSDLILKLKPYTTLALVGK
PELGILARDGQFARMVNKIRSTTDLIPIFANNLKSSNKYVINQNLDDIEV
YLRRKQTERSIDFTPSDITLVLGALLDTSHKFRNLDKDLCEKCAKCISMI
GVLDVTKHEFKRTTYSENEVYDLNDSVQTIKFLIWVINDILVPAFWQSEN
PSKQLFVALVIQESLKYCGLSSESWDMNHKELYPNEAKLWEKFNSVSKTT
IYPLLSSLYLAQSWKEYVPLKYPSNNFKEGYKIWVKRFTLDLLKTGTTEN
HPLHVFSSLIREDDGSLSNFLLPYISLDIIIKAEKGTPYADILNGIIIEF
DSIFTCNLEGMNNLQVDSLRMCYESIFRVFEYCKKWATEFKQNYSKLHGT
FIIKDTKTTNMLLRIDEFLRTTPSDLLAQRSLETDSFERSALYLEQCYRQ
NPHDKNQNGQLLKNLQITYEEIGDIDSLDGVLRTFATGNLVSKIEELQYS
ENWKLAQDCFNVLGKFSDDPKTTTRMLKSMYDHQLYSQIISNSSFHSSDG
KISLSPDVKEWYSIGLEAANLEGNVQTLKNWVEQIESLRNIDDREVLLQY
NIAKALIAISNEDPLRTQKYIHNSFRLIGTNFITSSKETTLLKKQNLLMK
LHSLYDLSFLSSAKDKFEYKSNTTILDYRMERIGADFVPNHYILSMRKSF
DQLKMNEQADADLGKTFFTLAQLARNNARLDIASESLMHCLERRLPQAEL
EFAEILWKQGENDRALKIVQEIHEKYQENSSVNARDRAAVLLKFTEWLDL
SNNSASEQIIKQYQDIFQIDSKWDKPYYSIGLYYSRLLERKKAEGYITNG
RFEYRAISYFLLAFEKNTAKVRENLPKVITFWLDIAAASISEAPRKEMLS
KATEDICSHVEEALQHCPTYIWYFVLTQLLSRLLHSHQSSAQIIMHILLS
LAVEYPSHILWYITALVNSNSSKRVLRGKHILEKYRQHSQNPHDLVSSAL
DLTKALTRVCLQDVKFKFDMNVAPSAMVVPVRKNLDIISPLEGYQPFRPV
VSIIRFGSSYKVFSSLKKPKQLNIIGSDGNIYGIMCKKEDVRQDNQYMQF
ATTMDFLLSKDIASRKRSLGINIYSVLSLREDCGILEMVPNVVTLRSILS
TKYESLKIKYSLKSLHDRWQHTAVDGKLEFYMEQVDKFPPILYQWFLENF
PDPINWFNARNTYARSYAVMAMVGHILGLGDRHCENILLDIQTGKVLHVD
LDCLFEKGKRLPVPEIVPFRLTPNLLDALGIIGTEGTFKKSSEVTLALMR
KNEVALMNVIETIMYDRNMDHSIQKALKVLRNKIRGIDPQDGLVLSVAGQ
TETLIQEATSEDNLSKMYIGWLPFW
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 chain6z2x Chain F Residue 2401 [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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PDB6z2x Mechanism of auto-inhibition and activation of Mec1 ATR checkpoint kinase.
Resolution3.2 Å
Binding residue
(original residue number in PDB)		S2058 P2062 K2080 E2130 M2131 H2226 E2228 N2229 V2242 D2243
Binding residue
(residue number reindexed from 1)		S2015 P2019 K2037 E2087 M2088 H2183 E2185 N2186 V2199 D2200
Annotation score3
Enzymatic activity
Enzyme Commision number 2.7.11.1: non-specific serine/threonine protein kinase.
Gene Ontology
Molecular Function
GO:0004672 protein kinase activity
GO:0004674 protein serine/threonine kinase activity
GO:0005515 protein binding
GO:0005524 ATP binding
GO:0016301 kinase activity
GO:0044024 histone H2AS1 kinase activity
GO:0106310 protein serine kinase activity
Biological Process
GO:0000077 DNA damage checkpoint signaling
GO:0000722 telomere maintenance via recombination
GO:0000723 telomere maintenance
GO:0006139 nucleobase-containing compound metabolic process
GO:0006260 DNA replication
GO:0006281 DNA repair
GO:0006310 DNA recombination
GO:0006325 chromatin organization
GO:0006338 chromatin remodeling
GO:0007131 reciprocal meiotic recombination
GO:0016310 phosphorylation
GO:0019222 regulation of metabolic process
GO:0033554 cellular response to stress
GO:0035556 intracellular signal transduction
GO:0042770 signal transduction in response to DNA damage
GO:0051321 meiotic cell cycle
GO:2000105 positive regulation of DNA-templated DNA replication
GO:2000779 regulation of double-strand break repair
Cellular Component
GO:0005634 nucleus
GO:0005694 chromosome
GO:0005739 mitochondrion
GO:0070310 ATR-ATRIP complex

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:6z2x, PDBe:6z2x, PDBj:6z2x
PDBsum6z2x
PubMed33169019
UniProtP38111|ATR_YEAST Serine/threonine-protein kinase MEC1 (Gene Name=MEC1)

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