Structure of PDB 6pur Chain D Binding Site BS02

Receptor Information
>6pur Chain D (length=1306) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
QESLSSWIPENIKKKECVYFVESSKLSDAGKVVCQCGYTHEQHLEEATKP
HTFQGTQWDPKKHVQEMPTDAFGDIVFTGLSQKVKKYVRVSQDTPSSVIY
HLMTQHWGLDVPNLLISVTGGAKNFNMKPRLKSIFRRGLVKVAQTTGAWI
ITGGSHTGVMKQVGEAVRDFSLSSSYKEGELITIGVATWGTVHRREGLIH
PTGSFPAEYILDEDGQGNLTCLDSNHSHFILVDDGTHGQYGVEIPLRTRL
EKFISEQTKERGGVAIKIPIVCVVLEGGPGTLHTIDNATTNGTPCVVVEG
SGRVADVIAQVANLPVSDITISLIQQKLSVFFQEMFETFTESRIVEWTKK
IQDIVRRRQLLTVFREGKDGQQDVDVAILQALLKASRSQDHFGHENWDHQ
LKLAVAWNRVDIARSEIFMDEWQWKPSDLHPTMTAALISNKPEFVKLFLE
NGVQLKEFVTWDTLLYLYENLDPSCLFHSKLQKVLVEDPERPACAPAAPR
LQMHHVAQVLRELLGDFTQPLYPRPRHGHVTFTMDPIRDLLIWAIVQNRR
ELAGIIWAQSQDCIAAALACSKILKELSKEEEDTDSSEEMLALAEEYEHR
AIGVFTECYRKDEERAQKLLTRVSEAWGKTTCLQLALEAKDMKFVSHGGI
QAFLTKVWWGQLSVDNGLWRVTLCMLAFPLLLTGLISFREKRLQDVGTPA
ARARAFFTAPVVVFHLNILSYFAFLCLFAYVLMVDFQPVPSWCECAIYLW
LFSLVCEEMRQLFYDPDECGLMKKAALYFSDFWNKLDVGAILLFVAGLTC
RLIPATLYPGRVILSLDFILFCLRLMHIFTISKTLGPKIIIVKRMMKDVF
FFLFLLAVWVVSFGVAKQAILIHNERRVDWLFRGAVYHSYLTIFGFPEWL
TVLLLCLYLLFTNILLLNLLIAMFNYTFQQVQEHTDQIWKFQRHDLIEEY
HGRPAAPPPFILLSHLQLFIKRVVLKRHKQLKNKLEKNEEAALLSWEIYL
KENYLQNRQFQQKQRPEQKIEDISNKVDAMVDLLDLDGDSYHVNARHLLY
PNCPVTRFPVPNEKVPWETEFLIYDPPFYTAERKDAAAMDPMGDTLEPLS
TIQYNVVDGLRDRRSFHGPYTVQAGLPLNPMGRTGLRGRGSLSCFGPNHT
LYPMVTRWRRNEDGAICRKSIKKMLEVLVVKLPLSEHWALPGGSREPGEM
LPRKLKRILRQEHWPSFENLLKCGMEVYKGYMDDPRNTDNAWIETVAVSV
HFQDQNDVELNRLNSNLHACDSGASIRWQVVDRRIPLYANHKTLLQKAAA
EFGAHY
Ligand information
Ligand IDAPR
InChIInChI=1S/C15H23N5O14P2/c16-12-7-13(18-3-17-12)20(4-19-7)14-10(23)8(21)5(32-14)1-30-35(26,27)34-36(28,29)31-2-6-9(22)11(24)15(25)33-6/h3-6,8-11,14-15,21-25H,1-2H2,(H,26,27)(H,28,29)(H2,16,17,18)/t5-,6-,8-,9-,10-,11-,14-,15-/m1/s1
InChIKeySRNWOUGRCWSEMX-KEOHHSTQSA-N
SMILES
SoftwareSMILES
ACDLabs 10.04O=P(O)(OCC3OC(n1c2ncnc(N)c2nc1)C(O)C3O)OP(=O)(O)OCC4OC(O)C(O)C4O
OpenEye OEToolkits 1.5.0c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)CO[P@](=O)(O)O[P@](=O)(O)OC[C@@H]4[C@H]([C@H]([C@@H](O4)O)O)O)O)O)N
OpenEye OEToolkits 1.5.0c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(O)OP(=O)(O)OCC4C(C(C(O4)O)O)O)O)O)N
CACTVS 3.341Nc1ncnc2n(cnc12)[CH]3O[CH](CO[P](O)(=O)O[P](O)(=O)OC[CH]4O[CH](O)[CH](O)[CH]4O)[CH](O)[CH]3O
CACTVS 3.341Nc1ncnc2n(cnc12)[C@@H]3O[C@H](CO[P@@](O)(=O)O[P@@](O)(=O)OC[C@H]4O[C@@H](O)[C@H](O)[C@@H]4O)[C@@H](O)[C@H]3O
FormulaC15 H23 N5 O14 P2
NameADENOSINE-5-DIPHOSPHORIBOSE
ChEMBLCHEMBL1231026
DrugBank
ZINCZINC000017654550
PDB chain6pur Chain D Residue 1602 [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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PDB6pur Ligand recognition and gating mechanism through three ligand-binding sites of human TRPM2 channel.
Resolution4.4 Å
Binding residue
(original residue number in PDB)		L1381 S1382 D1431 R1433 Y1485 N1487
Binding residue
(residue number reindexed from 1)		L1184 S1185 D1234 R1236 Y1288 N1290
Annotation score5
Enzymatic activity
Enzyme Commision number ?
Gene Ontology
Molecular Function
GO:0005216 monoatomic ion channel activity
GO:0005261 monoatomic cation channel activity
GO:0005262 calcium channel activity
GO:0005272 sodium channel activity
GO:0005384 manganese ion transmembrane transporter activity
GO:0005509 calcium ion binding
GO:0015278 intracellularly gated calcium channel activity
GO:0016787 hydrolase activity
GO:0046872 metal ion binding
GO:0047631 ADP-ribose diphosphatase activity
GO:0072571 mono-ADP-D-ribose binding
GO:0099604 ligand-gated calcium channel activity
Biological Process
GO:0001659 temperature homeostasis
GO:0002407 dendritic cell chemotaxis
GO:0006811 monoatomic ion transport
GO:0006814 sodium ion transport
GO:0006816 calcium ion transport
GO:0006828 manganese ion transport
GO:0009408 response to heat
GO:0014074 response to purine-containing compound
GO:0019722 calcium-mediated signaling
GO:0032956 regulation of actin cytoskeleton organization
GO:0033194 response to hydroperoxide
GO:0035725 sodium ion transmembrane transport
GO:0051209 release of sequestered calcium ion into cytosol
GO:0051289 protein homotetramerization
GO:0051489 regulation of filopodium assembly
GO:0055085 transmembrane transport
GO:0070301 cellular response to hydrogen peroxide
GO:0070588 calcium ion transmembrane transport
GO:0071277 cellular response to calcium ion
GO:0071421 manganese ion transmembrane transport
GO:0071502 cellular response to temperature stimulus
GO:0071577 zinc ion transmembrane transport
GO:0097028 dendritic cell differentiation
GO:0097553 calcium ion transmembrane import into cytosol
GO:0098703 calcium ion import across plasma membrane
Cellular Component
GO:0005764 lysosome
GO:0005765 lysosomal membrane
GO:0005886 plasma membrane
GO:0016020 membrane
GO:0030659 cytoplasmic vesicle membrane
GO:0031410 cytoplasmic vesicle
GO:0035579 specific granule membrane
GO:0042995 cell projection
GO:0043204 perikaryon
GO:0070821 tertiary granule membrane
GO:0101003 ficolin-1-rich granule membrane

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:6pur, PDBe:6pur, PDBj:6pur
PDBsum6pur
PubMed31513012
UniProtO94759|TRPM2_HUMAN Transient receptor potential cation channel subfamily M member 2 (Gene Name=TRPM2)

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