Structure of PDB 7cba Chain A Binding Site BS04

Receptor Information
>7cba Chain A (length=768) Species: 8656 (Naja atra) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
QDICVLPTQSWSCNKLRCGEKRMANVLCSCSEDCLTKKDCCTDYKSICKR
ETSWLKDQCASSQCPEGFDQSPLILFSMDGFRAEYLETWDTLMPNINKLK
TCGTHAKYMRAVYPTKTFVNHYTIVTGLYAETHGIIDNNMYDVKLNQNFS
LSGSNMRNAAWWGGQPIWHTASYQGLKAATYFWPGSEVKINGSYPTIYKV
YNKSTPFEARVMEVLKWLDLPKAKRPDFSTLYIEEPDTTGHKFGPVSGQV
IKSLQMADRTLGMLMEGLKQRNLHNCVNLILLADHGMEAISCNRLEYMTD
YFNTVDFFMYEGAAPRIRSKNVPKDFYTFDSEAIVKKLTCRKPKQHFKAY
LAKDLPKRLHFANNIRIDKVNLMVDRQWLAVRNKKCSGGTHGYDNEFKSM
EAIFLAHGPGFKEKTEVTSFENIEVYNLMCDLLKLKPAPNNGTHGSLNHL
LKNPFYNPSPAKEQSPPLYCLFGPVPSPDVSGCKCSSITDLEAVNQRLNL
IDQAKMQSEADNLPYGRPHVLQHSKYCLLHQTKYISAYSQDILMPLWNSY
TISKSLDCLRLDVRIPTVQSQTCSNYQPDLAITPGFLYPPDFSSSGPEQY
DALITSNIVPMYKEFARLWNYFHSTLLPKYATERNGLNVISGPIFDYNYD
GHFDPYDTIDQYVNNTKIPIPTHYFVVLTSCENSTKTPLNCPPGSLKVLS
FILPHRPDNSESCADKSPDNLWVEERMQTHTARVRDVELLTGLDFYSALK
QPLSETLRLKTFLPIFIN
Ligand information
Ligand IDIRH
InChIInChI=1S/C16H12O7/c1-22-11-4-7(2-3-9(11)18)16-15(21)14(20)13-10(19)5-8(17)6-12(13)23-16/h2-6,17-19,21H,1H3
InChIKeyIZQSVPBOUDKVDZ-UHFFFAOYSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 2.0.6COc1cc(ccc1O)C2=C(C(=O)c3c(cc(cc3O2)O)O)O
ACDLabs 12.01COc1c(O)ccc(c1)C=3Oc2cc(O)cc(c2C(C=3O)=O)O
CACTVS 3.385COc1cc(ccc1O)C2=C(O)C(=O)c3c(O)cc(O)cc3O2
FormulaC16 H12 O7
Nameisorhamnetin;
3,5,7-trihydroxy-2-(4-hydroxy-3-methoxyphenyl)-4H-1-benzopyran-4-one
ChEMBLCHEMBL379064
DrugBankDB16767
ZINCZINC000000517261
PDB chain7cba Chain A Residue 908 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB7cba Crystal structure of snake venom phosphodiesterase (PDE) from Taiwan cobra (Naja atra atra) in complex with isorhamnetin and citrate
Resolution2.901 Å
Binding residue
(original residue number in PDB)		F186 W251 P252 Y269 K271 Y300 E302 D305 T306
Binding residue
(residue number reindexed from 1)		F118 W183 P184 Y201 K203 Y232 E234 D237 T238
Annotation score1
Enzymatic activity
Enzyme Commision number 3.6.1.-
Gene Ontology
Molecular Function
GO:0003676 nucleic acid binding
GO:0016787 hydrolase activity
GO:0043262 ADP phosphatase activity
GO:0046872 metal ion binding
GO:0047429 nucleoside triphosphate diphosphatase activity
GO:0090729 toxin activity
Biological Process
GO:0009143 nucleoside triphosphate catabolic process
GO:0035821 modulation of process of another organism
Cellular Component
GO:0005576 extracellular region

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:7cba, PDBe:7cba, PDBj:7cba
PDBsum7cba
PubMed
UniProtA0A2D0TC04|PDE_NAJAT Venom phosphodiesterase

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