Structure of PDB 7vfw Chain A Binding Site BS01

Receptor Information

>7vfw Chain A (length=1266) Species: 9606 (Homo sapiens)

NVVRKYAKRITEWPPFEYMILATIIANCIVLALEQHLPDGDKTPMSERLD
DTEPYFIGIFCFEAGIKIIALGFVFHKGSYLRNGWNVMDFVVVLTGILAT
AGTDFDLRTLRAVRVLRPLKLVSGIPSLQVVLKSIMKAMVPLLQIGLLLF
FAILMFAIIGLEFYMGKFHKACFPNSTDAEPVGDFPCGKEAPARLCEGDT
ECREYWPGPNFGITNFDNILFAILTVFQCITMEGWTDILYNTNDAAGNTW
NWLYFIPLIIIGSFFMLNLVLGVLSGEFAKERERVENRRAFLKLRRQQQI
ERELNGYLEWIFKAEEVMLAEEDRNSYFRRKEKMFRFFIRRMVKAQSFYW
VVLCVVALNTLCVAMVHYNQPRRLTTTLYFAEFVFLGLFLTEMSLKMYGL
GPRSYFRSSFNCFDFGVIVGSVFEVVWAAIKPGSSFGISVLRALRLLRIF
KVTKYWSSLRNLVVSLLNSMKSIISLLFLLFLFIVVFALLGMQLFGGQFN
FQDETPTTNFDTFPAAILTVFQILTGEDWNAVMYHGIESQGGVSKGMFSS
FYFIVLTLFGNYTLLNVFLAIAVDNLANAQELTKDEEEMEEAANQKLALQ
KAKEVAARSVWEQRASQLRLQNLRASRRFCHYIVTMRYFEVVILVVIALS
SIALAAEDPVRTDSPRNNALKYLDYIFTGVFTFEMVIKMIDLGLLLHPGA
YFRDLWNILDFIVVSGALVAFAFSGSKGKDINTIKSLRVLRVLRPLKTIK
RLPKLKAVFDCVVNSLKNVLNILIVYMLFMFIFAVIAVQLFKGKFFYCTD
ESKELERDCRGQYLDYEKEEVEAQPRQWKKYDFHYDNVLWALLTLFTVST
GEGWPMVLKHSVDATYEEQGPSPGYRMELSIFYVVYFVVFPFFFVNIFVA
LIIITFQEQKNERACIDFAISAPQNRQSFQYKTWTFVVSPPFEYFIMAMI
ALNTVVLMMKFYDAPYEYELMLKCLNIVFTSMFSMECVLKIIAFGVLNYF
RDAWNVFDFVTVLGSITDILVTEIAETNNFINLSFLRLFRAARLIKLLRQ
GYTIRILLWTFVQSFKALPYVCLLIAMLFFIYAIIGMQVFGNIALDDDTS
INRHNNFRTFLQALMLLFRSATGEAWHEIMLSCLSNQACDEQANATECGS
DFAYFYFVSFIFLCSFLMLNLFVAVIMDNFEYLTRDSSILGPHHLDEFIR
VWANDMFEMLKHMSVHFTSTLMALIRTALEITKQHQCDAELRKEISVVWA
NLPQKTLDLLVPPHKP

Ligand information

• Ligand ID: Y01
• InChI: InChI=1S/C31H50O4/c1-20(2)7-6-8-21(3)25-11-12-26-24-10-9-22-19-23(35-29(34)14-13-28(32)33)15-17-30(22,4)27(24)16-18-31(25,26)5/h9,20-21,23-27H,6-8,10-19H2,1-5H3,(H,32,33)/t21-,23+,24+,25-,26+,27+,30+,31-/m1/s1
• InChIKey: WLNARFZDISHUGS-MIXBDBMTSA-N
• SMILES:
  CACTVS 3.352: CC(C)CCC[C@@H](C)[C@H]1CC[C@H]2[C@@H]3CC=C4C[C@H](CC[C@]4(C)[C@H]3CC[C@]12C)OC(=O)CCC(O)=O
  OpenEye OEToolkits 1.6.1: CC(C)CCCC(C)C1CCC2C1(CCC3C2CC=C4C3(CCC(C4)OC(=O)CCC(=O)O)C)C
  OpenEye OEToolkits 1.6.1: CC(C)CCC[C@@H](C)[C@H]1CC[C@@H]2[C@@]1(CC[C@H]3[C@H]2CC=C4[C@@]3(CC[C@@H](C4)OC(=O)CCC(=O)O)C)C
  CACTVS 3.352: CC(C)CCC[CH](C)[CH]1CC[CH]2[CH]3CC=C4C[CH](CC[C]4(C)[CH]3CC[C]12C)OC(=O)CCC(O)=O
• Formula: C31 H50 O4
• Name: CHOLESTEROL HEMISUCCINATE
• ZINC: ZINC000058638837
• PDB chain: 7vfw Chain A Residue 2403

Receptor-Ligand Complex Structure

Structure summary

• PDB: 7vfw Closed-state inactivation and pore-blocker modulation mechanisms of human Ca V 2.2.
• Resolution: 3.3 Å
• Binding residue (original residue number in PDB): T496 A500 N1350 V1351
• Binding residue (residue number reindexed from 1): T360 A364 N837 V838
• Annotation score: 1

Gene Ontology

Molecular Function

• GO:0001540 amyloid-beta binding
• GO:0005216 monoatomic ion channel activity
• GO:0005245 voltage-gated calcium channel activity
• GO:0005262 calcium channel activity
• GO:0005509 calcium ion binding
• GO:0005515 protein binding
• GO:0005524 ATP binding
• GO:0008331 high voltage-gated calcium channel activity
• GO:0046872 metal ion binding

Biological Process

• GO:0006811 monoatomic ion transport
• GO:0006816 calcium ion transport
• GO:0007268 chemical synaptic transmission
• GO:0050804 modulation of chemical synaptic transmission
• GO:0055085 transmembrane transport
• GO:0070588 calcium ion transmembrane transport
• GO:0098703 calcium ion import across plasma membrane
• GO:1904645 response to amyloid-beta

Cellular Component

• GO:0005886 plasma membrane
• GO:0005891 voltage-gated calcium channel complex
• GO:0016020 membrane
• GO:0034702 monoatomic ion channel complex
• GO:0043025 neuronal cell body
• GO:0045202 synapse

External links

• PDB: RCSB:7vfw, PDBe:7vfw, PDBj:7vfw
• PDBsum: 7vfw
• PubMed: 34731621
• UniProt: Q00975|CAC1B_HUMAN Voltage-dependent N-type calcium channel subunit alpha-1B (Gene Name=CACNA1B)