Structure of PDB 6drj Chain D Binding Site BS01

Receptor Information

>6drj Chain D (length=1266) Species: 7955 (Danio rerio)

CSLASWIKENIKKKECVRETPTDAFGDISFGGLGQKTGKYVRVSSDTSCE
NLYQLMTEQWKLRSPNLLISVTGGAKNFYIKTHLKDKFRRGLIKVAQTTG
AWILTGGTHAGVMKHVGMAVRDYTLSSGSMEGQIVVIGVAPWGVIHNRST
LIHPEGRFPAYYSLDEQGQGRLSCLDINHTHFLLVDDGTQGHYGVEIELR
ARLEKLISKLSLGNRESGVTIPVVCVVLDGGPGTLNTIYNSMLNHTPCVV
LEGSGRLADVIAHVASVPVSKVTMALINRLLKRFFMQEYKNFTELQIIEW
TKKIQDILRMPHLLTVFRIDEDKNYDVDVAILQALLKASRSDEHAGRHCW
ERQLELAVAWNRVDIAESEIFTEESQWTSSDLHPAMFSALVGDKPEFVRL
LLENGVCVREFLEREETLCELYSHLPSCFFLRKLAKRVQGLPGSRKVCLS
HVSEEVRHLLGSFTQPLYIASRYKPADTVWDPGRDLFLWAVVQNNRELAE
IGWEQCRDCIAAALAASKILRKLAQESGEDDSEEATEMLELANHYEKQAI
GVFSECHSWDAQRAQKLLIRISPSWGRSTCLWLALEAHDKSFIAHSGVQA
LLTQIWCGELSVDNPHWKVLLCMIFFPLIYTGFLTFRRDEDIQRQAERTQ
QKLLKPLNCSSRLMSFLKSPQVKFYWNIASYFGFLWLFAVVLMIDFQTSP
SWRELLLYVWLTSLVCEEIRQLYHDFDGSGFRRKAKMYIKDLWNILDVLS
IVLFIAGLICRLQASDTVFYIGKVILCIDFIIFCLRLMAIFSISRTLGPK
IIIVRRMMLDLFFFMFLLSIWVVAYGVAKQGILIENEERLNWIIRGAVYE
PYITIFGNFPTNIDNTLFDISSCSVNASDPLKPKCPMLNADNTPVFPEWL
TIMMLCVYLLFANILLLNLLIAIFNYTFQEVQDNTDTIWKFQRYELIKEY
HSRPALPPPFILLSHLILFIRGVFLRDLPQRHKNFRQELEQTEEEELLSW
EAYMKDNYLASTRQDESQSVEHRIHDTAEKVGAMSELLEREQEMVDEEAP
HMFARQLQYPDSTVRRFPVPEEKVSWEVNFSPYQPPVYNQQALDKHRNPG
GRTGIRGKGALNTLGPNHILHPIFTRWRDAEHKVLEFLAVWEDAEKRWAL
LGGPAQPDEPLAQVLERILGKKLNEKTKTLLKAGEEVYKGYVDDSRNTDN
AWVETSIITLHCDKNTPLMADLNHMVESSLSSHQPLQWREVSSDACRCSY
QREALRQIAHHHNTYF

Ligand information

• Ligand ID: APR
• InChI: InChI=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
• InChIKey: SRNWOUGRCWSEMX-KEOHHSTQSA-N
• SMILES:
  ACDLabs 10.04: O=P(O)(OCC3OC(n1c2ncnc(N)c2nc1)C(O)C3O)OP(=O)(O)OCC4OC(O)C(O)C4O
  OpenEye OEToolkits 1.5.0: c1nc(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 1.5.0: c1nc(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 3.341: Nc1ncnc2n(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 3.341: Nc1ncnc2n(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
• Formula: C15 H23 N5 O14 P2
• Name: ADENOSINE-5-DIPHOSPHORIBOSE
• ChEMBL: CHEMBL1231026
• ZINC: ZINC000017654550
• PDB chain: 6drj Chain D Residue 2001

Receptor-Ligand Complex Structure

Structure summary

• PDB: 6drj Architecture of the TRPM2 channel and its activation mechanism by ADP-ribose and calcium.
• Resolution: 3.3 Å
• Binding residue (original residue number in PDB): T150 G151 A153 T186 Y271 R278 G309 G311 T312
• Binding residue (residue number reindexed from 1): T72 G73 A75 T108 Y193 R200 G231 G233 T234
• Annotation score: 5

Gene Ontology

Molecular Function

• GO:0005216 monoatomic ion channel activity
• GO:0005262 calcium channel activity
• GO:0005509 calcium ion binding
• GO:0046872 metal ion binding
• GO:0047631 ADP-ribose diphosphatase activity
• GO:0072570 ADP-D-ribose binding
• GO:0072571 mono-ADP-D-ribose binding
• GO:0099094 ligand-gated monoatomic cation channel activity
• GO:0099604 ligand-gated calcium channel activity

Biological Process

• GO:0006811 monoatomic ion transport
• GO:0019722 calcium-mediated signaling
• GO:0051289 protein homotetramerization
• GO:0055085 transmembrane transport
• GO:0070588 calcium ion transmembrane transport

Cellular Component

• GO:0005886 plasma membrane
• GO:0016020 membrane

External links

• PDB: RCSB:6drj, PDBe:6drj, PDBj:6drj
• PDBsum: 6drj
• PubMed: 30250252
• UniProt: A0A0R4IMY7|TRPM2_DANRE Transient receptor potential cation channel subfamily M member 2 (Gene Name=trpm2)