Structure of PDB 7r78 Chain A Binding Site BS09

Receptor Information
>7r78 Chain A (length=1880) Species: 235443 (Cryptococcus neoformans var. grubii H99) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
DDLPPISDIEAMFDHLVSRIPDIVELVRQLNGRKLRVATMCSGTESPLLA
LNMIAKAIKAQHGLTLAFEHVFSCEIEPFKQAYIERNFTPPILFRDVTEL
GKKRAHTAYGSMVDVPGDVDILIAGTSCVDYSNLNNVQQDIDANGESGRT
FRGMLQWVKKHQPPIVILENVCNAPWDKVVEYFGQIDYDAQYTRLDTKEF
YIPHTRTRVYLFATPSSSESDDLPEKWAQTVKDLRRPWSSPFEAFLLHTD
DPNIHRARLELASARAGTSRKTTDWNRCESRHQRARQDEALGLLRPLTSW
QEAGVCKGLDWTWNDWLLAQTERVVDLLEISTLRMAKDGIDSGFKACIWN
VSQNVDRQTGSSKTALAPCLTPNMIPWVTIRGGPVTGREALALQGIPVRE
LLLTSENEDQLADLAGNAMTTTVVGSAMIAALKVACHKITEGANPEKEAA
LILEKEAVDDEQVANRIIGEDYLEHHDLDLAKVTKSNLSEILDLACRSSR
HCQCEGQSGTAPNILECQECSYRACKSCGGRPEHVYAPCANQRVEPAEFE
KRFKGLLPMRVRIAGLTDQCLNAVRKAAEKSNKGSVNDNDWQLWSTALLE
GIHDAEFRFRYLKRQSTWTAVYEARRAMLSLVLRNQIPEWRLTIKAPASE
PNNSQLRALLLHPVARLQIDIAGQDVLCGPWELCIPSMKTIDIEITGKGE
LLPSWQASLGLQGPFANTTRWSEVEISLQAEDENTLDRKLSGTYQLLPRC
GQAMSSLHKKRPDLSDDGLPQLYFFLDPTRCGESREDRYVFSTSTERLDY
GTERPVIARLDSHWREGNEKQRKVKLDVSGAWVKCPEAHLTAIRATFAIP
SSASAISASLTTEGCSHAMALLSCRVPLDPTHSESMWRRGAWAEIDLSHQ
GNTTFANLAWITERLPPLDGLKNWAHIADDVSEHVCERCAPRPPKIHWIK
RAFEDKLEAGQYEHALKHRPSPFVVQLRLDQDIGSFRIGLNIVSLAHRAL
SRLPPTTSEHKISLSWRLTPGHVTESPQPRRVFILPSNKQDPENSQPEAF
KLPLRKEQLRSLWWMLEQEKATGKTHTFVEEEISESLLPAVGWRAEGKAE
RPVMVRGGVIADQVGYGKTVISIALVAQTLSLPAPEPATPGLIDLKATLI
VVPGHLSKQWPNEIARFTGSMFKVIVIQGMKDLQEKTIAELGKADIIVMA
SEIFESDVYWSRLEYLSAQPREWLHDTQGGRFFCDRLDAAMESLVSQTKI
LKEKGSEAAMRAMEDKKKSLVDNVGSKKEVHTKLLPNPVLHMFRFRRVIA
DEFTYLQKKSLAAVLRLSSSYRWILSGTPPVSDFAAIRSIATFMGIHLGV
EDDGEGDDQTQAEKFHAFREVHSRAWHNRRDELAQEFLNVFVRQNIAEIE
DIPTVEHIHTFKLPASEGAVYLELEHHLQALEMQARKENVSQGDRNARLE
EALSDSKTAEEALLKRCCHFTLDLSDKTQDAKSAQEACDHITSARARQLL
ACQEDLSRSVNQAIALHGWIKKKGGFSKNDDERQPFAEWIAFSSNISKHQ
GDIEAARILLKVIEKCGVKDGNIPPSPSDKQSPSIASGAKMDDVKWQLRE
QTHLLRKLVKELVARVRSLRFFEVVRKIQKGKSDAQIVLESSECGHKPST
NPDIEMAILSCCGHVACHKCMRKAAASQRCVKSGECQAAVRPTNIVKVSS
LGVEGELSSGRYGAKLEHLVNLIHSIPKNERVLVFLQWEDLAGKVSEALS
AGRIPHVTLSGSAKSRANTLDRFQSTNADSARVLLLKMNDASAAGSNLTT
ANHAVFLGPLFTNSLFNYRAVETQAIGRVRRYGQQKKVHIHRLLALDTID
MTIFNARRTELKEKTDWEEIPQEEYKGRGS
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 chain7r78 Chain A Residue 2407 [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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PDB7r78 Structural insights into DNMT5-mediated ATP-dependent high-fidelity epigenome maintenance.
Resolution3.5 Å
Binding residue
(original residue number in PDB)		R1406 Q1409 V1465 Y1467 G1468 K1469 T1470 V1471 E1514 R1517 N2234 R2265 R2268
Binding residue
(residue number reindexed from 1)		R1055 Q1058 V1114 Y1116 G1117 K1118 T1119 V1120 E1163 R1166 N1797 R1828 R1831
Annotation score3
Enzymatic activity
Enzyme Commision number 3.6.4.-
Gene Ontology
Molecular Function
GO:0003677 DNA binding
GO:0003682 chromatin binding
GO:0003886 DNA (cytosine-5-)-methyltransferase activity
GO:0005524 ATP binding
GO:0008094 ATP-dependent activity, acting on DNA
GO:0008168 methyltransferase activity
GO:0016787 hydrolase activity
GO:0016887 ATP hydrolysis activity
GO:0043565 sequence-specific DNA binding
GO:0120328 ATP-dependent DNA (cytosine-5-)-methyltransferase activity
GO:0140658 ATP-dependent chromatin remodeler activity
Biological Process
GO:0006289 nucleotide-excision repair
GO:0006338 chromatin remodeling
GO:0006346 DNA methylation-dependent heterochromatin formation
GO:0009889 regulation of biosynthetic process
GO:0032259 methylation
Cellular Component
GO:0005634 nucleus
GO:0005694 chromosome

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:7r78, PDBe:7r78, PDBj:7r78
PDBsum7r78
PubMed35202575
UniProtJ9VI03|DMT5_CRYNH DNA (cytosine-5-)-methyltransferase DMT5 (Gene Name=DMT5)

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