Structure of PDB 8agd Chain B Binding Site BS02

Receptor Information
>8agd Chain B (length=1111) Species: 243230 (Deinococcus radiodurans R1 = ATCC 13939 = DSM 20539) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
VSRGVILGYPDGTFRGTQNLTRYEAAIIIARLLDQMRDGETPAGMTAEDM
TALQNAIQELAADLAALGVRVSDLEANAVSKDDFARLEARIEEVAAAGGE
QGATEALQGRVDEYDALRADVDDNASSIAALNDLTVLLNQDILDLQDRVS
AVEAAQADFVQRSDFDALGGRVTTVETRVETVNNSLTGRIAALERNAFSV
KPSLTIGYSVSRTSRNFDVDRLFPLNADGTVANNAFTSGGIDTDTGAQRR
DFGDFGNASDPVVAGAAGLYGFADGVSYTVYFTDGSTATFDGLNPADYKV
PTGKVIDTTKGRNGFGFNNLARYKEGSTDIGISLGFDTSGQFSQVTSGTG
GSLFSTAGRLQVNQIDLNFGLVTGLPSDAYVDTNGNGKKDDGEATGRGTY
LGSGGTAAILRDPAGNVYRPVFFRFKNATTQFSVGNNPVIVTLGQQQKFY
FSDYVFDNNYDGRGDGFTVTVDGSNVPVIGAWKPQIKGVYGSRSGLDGTA
EAGYGVYYRGVRAQITPVGTLTAGIHYAQEGRDMFGAAQNTTSTPSDVTT
YGADLHGKAFGVELHSEYATSRVRPNTANAAVQTSNAFYARVATRKDNLA
FDLNTPAAKFGNDTFGVSLYDLNYRKIDAGYNNVAGISEYGYGSYSRTSA
QNIAYNPDTGVTAPFANLDRQAYTDANNDGTSDRNADGTVVATNTKIGQM
GFGVKAAANLGPVAIGGYYDTSTGANGDNANRMTEAGGSAKVAYSIFSLR
GTYNTLDSNRPQIYRDAAGTQIIGDAKVRRYAVQADVTPGLGLFVGAYYR
DVNVNGVRSTTDRGLLGRGYLASSFEPGVGNNAYRTGLRCADNNFGTGTR
DIDGVGGVLNPAVNLDQSRTATCFTSYGVEAGHAGDNANALVKDLFFRVG
YSRVYVPTTATATTGDFSGSVTYGDARYDRKVGVANVRLAGSFSTTNTQL
DSRPAGTRGAVGLIVRTDPLENVPFRPQFNGQVGYYTADNRVAAGNYNAN
ATKYGAGVVLNDFLLPQTKIGVRYDGYMAQNRQYTPFDGDGTQGYFSDAN
NNRRTNLNGVYVEGAYQDLIFSYGTYTLSQKDLNGVEYGSGINNGQPARG
QTFKISYKVNF
Ligand information
Ligand IDJPI
InChIInChI=1S/C40H80O3/c1-30(19-13-21-32(3)22-14-23-33(4)25-16-28-39(7,8)43)17-11-12-18-31(2)20-15-24-34(5)26-27-36-35(6)37(41)29-38(42)40(36,9)10/h30-38,41-43H,11-29H2,1-10H3/t30-,31+,32-,33-,34-,35+,36+,37-,38-/m0/s1
InChIKeyHMWJPEUVPLHAER-VMKFVPKQSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 2.0.7C[C@@H]1[C@H](C([C@H](CC1O)O)(C)C)CC[C@@H](C)CCC[C@H](C)CCCC[C@H](C)CCC[C@H](C)CCC[C@H](C)CCCC(C)(C)O
CACTVS 3.385C[CH](CCCC[CH](C)CCC[CH](C)CC[CH]1[CH](C)[CH](O)C[CH](O)C1(C)C)CCC[CH](C)CCC[CH](C)CCCC(C)(C)O
OpenEye OEToolkits 2.0.7CC1C(CC(C(C1CCC(C)CCCC(C)CCCCC(C)CCCC(C)CCCC(C)CCCC(C)(C)O)(C)C)O)O
CACTVS 3.385C[C@@H](CCCC[C@@H](C)CCC[C@H](C)CC[C@@H]1[C@@H](C)[C@@H](O)C[C@H](O)C1(C)C)CCC[C@H](C)CCC[C@H](C)CCCC(C)(C)O
FormulaC40 H80 O3
Name(3~{S},5~{R},6~{R})-5-[(3~{S},7~{R},12~{S},16~{S},20~{S})-3,7,12,16,20,24-hexamethyl-24-oxidanyl-pentacosyl]-4,4,6-trimethyl-cyclohexane-1,3-diol
ChEMBL
DrugBank
ZINC
PDB chain8agd Chain B Residue 1302 [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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PDB8agd The SDBC is active in quenching oxidative conditions and bridges the cell envelope layers in Deinococcus radiodurans.
Resolution3.5 Å
Binding residue
(original residue number in PDB)		P540 I542 I571 A579 A609 D610 S622
Binding residue
(residue number reindexed from 1)		P484 I486 I515 A523 A553 D554 S566
Annotation score1
Enzymatic activity
Enzyme Commision number ?
External links
PDB RCSB:8agd, PDBe:8agd, PDBj:8agd
PDBsum8agd
PubMed36502921
UniProtQ9RRB6|SLPA_DEIRA Outer membrane protein SlpA (Gene Name=slpA)

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