Structure of PDB 8agd Chain B Binding Site BS03

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 IDJPX
InChIInChI=1S/C48H91N2O15P/c1-5-9-12-15-17-18-19-20-21-22-24-27-30-33-49-47(57)40(37-61-48-44(50-41(52)8-4)46(56)45(55)39(34-51)64-48)65-66(58,59)62-36-38(63-43(54)32-29-25-14-11-7-3)35-60-42(53)31-28-26-23-16-13-10-6-2/h38-40,44-46,48,51,55-56H,5-37H2,1-4H3,(H,49,57)(H,50,52)(H,58,59)/t38-,39-,40-,44-,45+,46-,48-/m0/s1
InChIKeyBORXCJRMZBMSCX-GUINJWSRSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 2.0.7CCCCCCCCCCCCCCCNC(=O)C(COC1C(C(C(C(O1)CO)O)O)NC(=O)CC)OP(=O)(O)OCC(COC(=O)CCCCCCCCC)OC(=O)CCCCCCC
CACTVS 3.385CCCCCCCCCCCCCCCNC(=O)[CH](CO[CH]1O[CH](CO)[CH](O)[CH](O)[CH]1NC(=O)CC)O[P](O)(=O)OC[CH](COC(=O)CCCCCCCCC)OC(=O)CCCCCCC
OpenEye OEToolkits 2.0.7CCCCCCCCCCCCCCCNC(=O)[C@H](CO[C@@H]1[C@H]([C@@H]([C@@H]([C@@H](O1)CO)O)O)NC(=O)CC)OP(=O)(O)OC[C@H](COC(=O)CCCCCCCCC)OC(=O)CCCCCCC
CACTVS 3.385CCCCCCCCCCCCCCCNC(=O)[C@H](CO[C@H]1O[C@@H](CO)[C@@H](O)[C@@H](O)[C@@H]1NC(=O)CC)O[P](O)(=O)OC[C@H](COC(=O)CCCCCCCCC)OC(=O)CCCCCCC
FormulaC48 H91 N2 O15 P
Name[(2~{S})-3-[[(2~{S})-3-[(2~{S},3~{S},4~{S},5~{S},6~{S})-6-(hydroxymethyl)-4,5-bis(oxidanyl)-3-(propanoylamino)oxan-2-yl]oxy-1-oxidanylidene-1-(pentadecylamino)propan-2-yl]oxy-oxidanyl-phosphoryl]oxy-2-octanoyloxy-propyl] decanoate
ChEMBL
DrugBank
ZINC
PDB chain8agd Chain B Residue 1303 [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)
R268 V1118 G1120 Y1129 Q1157 F1159
Binding residue
(residue number reindexed from 1)
R212 V1062 G1064 Y1073 Q1101 F1103
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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