Structure of PDB 6smq Chain B Binding Site BS02

Receptor Information
>6smq Chain B (length=903) Species: 242619 (Porphyromonas gingivalis W83) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
LSTVSGSVAKVSSEKLAEKPVANIMDALQGQVAGMQVMTTSGDPTAVASV
EIHGTGSLGASSAPLYIVDGMQTSLDVVATMNPNDFESMSVLKDASATSI
YGARAANGVVFIQTKKGKMSERGRITFNASYGISQILNTKPLDNMMTGDE
LLDFQVKAGFWGNNQTVQKVKDMILAGAEDLYGNYDSLKDEYGKTLFPVD
FNHDADWLKALFKTAPTSQGDISFSGGSQGTSYYASIGYFDQEGMAREPA
NFKRYSGRLNFESRINEWLKVGANLSGAIANRRSADYFGKYYMGSGTFGV
LTMPRYYNPFDVNGDLADVYYMYGATRPSMTEPYFAKMRPFSSESHQANV
NGFAQITPIKGLTLKAQAGVDITNTRTSSKRMPNNPYDSTPLGERRERAY
RDVSKSFTNTAEYKFSIDEKHDLTALMGHEYIEYEGDVIGASSKGFESDK
LMLLSQGKTGNSLSLPEHRVAEYAYLSFFSRFNYGFDKWMYIDFSVRNDQ
SSRFGSNNRSAWFYSVGGMFDIYNKFIQESNWLSDLRLKMSYGTTGNSEI
GNYNHQALVTVNNYTEDAMGLSISTAGNPDLSWEKQSQFNFGLAAGAFNN
RLSAEVDFYVRTTNDMLIDVPMPYISGFFSQYQNVGSMKNTGVDLSLKGT
IYQNKDWNVYASANFNYNRQEITKLFFGLNKYMLPNTGTIWEIGYPNSFY
MAEYAGIDKKTGKQLWYVPGQVDADGNKVTTSQYSADLETRIDKSVTPPI
TGGFSLGASWKGLSLDADFAYIVGKWMINNDRYFTENGGGLMQLNKDKML
LNAWTEDNKETDVPKLGQSPQFDTHLLENASFLRLKNLKLTYVLPNSLFA
GQNVIGGARVYLMARNLLTVTKYKGFDPEAGGNVGKNQYPNSKQYVAGIQ
LSF
Ligand information
Ligand ID5PL
InChIInChI=1S/C67H129N2O15P/c1-7-8-9-10-11-12-13-14-15-16-17-18-25-30-35-40-45-50-68-66(76)60(54-80-67-63(69-57(6)71)65(75)64(74)59(51-70)83-67)84-85(77,78)81-53-58(82-62(73)49-44-39-34-29-24-20-22-27-32-37-42-47-56(4)5)52-79-61(72)48-43-38-33-28-23-19-21-26-31-36-41-46-55(2)3/h55-56,58-60,63-65,67,70,74-75H,7-54H2,1-6H3,(H,68,76)(H,69,71)(H,77,78)/t58-,59-,60-,63-,64-,65-,67+/m1/s1
InChIKeyLEQHPGOQHCQGAI-TYASGWLASA-N
SMILES
SoftwareSMILES
CACTVS 3.370CCCCCCCCCCCCCCCCCCCNC(=O)[C@@H](CO[C@H]1O[C@H](CO)[C@@H](O)[C@H](O)[C@H]1NC(C)=O)O[P](O)(=O)OC[C@@H](COC(=O)CCCCCCCCCCCCCC(C)C)OC(=O)CCCCCCCCCCCCCC(C)C
ACDLabs 12.01O=C(OCC(OC(=O)CCCCCCCCCCCCCC(C)C)COP(=O)(O)OC(C(=O)NCCCCCCCCCCCCCCCCCCC)COC1OC(C(O)C(O)C1NC(=O)C)CO)CCCCCCCCCCCCCC(C)C
OpenEye OEToolkits 1.7.2CCCCCCCCCCCCCCCCCCCNC(=O)C(COC1C(C(C(C(O1)CO)O)O)NC(=O)C)OP(=O)(O)OCC(COC(=O)CCCCCCCCCCCCCC(C)C)OC(=O)CCCCCCCCCCCCCC(C)C
CACTVS 3.370CCCCCCCCCCCCCCCCCCCNC(=O)[CH](CO[CH]1O[CH](CO)[CH](O)[CH](O)[CH]1NC(C)=O)O[P](O)(=O)OC[CH](COC(=O)CCCCCCCCCCCCCC(C)C)OC(=O)CCCCCCCCCCCCCC(C)C
OpenEye OEToolkits 1.7.2CCCCCCCCCCCCCCCCCCCNC(=O)[C@@H](CO[C@@H]1[C@@H]([C@H]([C@@H]([C@H](O1)CO)O)O)NC(=O)C)OP(=O)(O)OCC(COC(=O)CCCCCCCCCCCCCC(C)C)OC(=O)CCCCCCCCCCCCCC(C)C
FormulaC67 H129 N2 O15 P
Name(1R,4S,6R)-6-({[2-(ACETYLAMINO)-2-DEOXY-ALPHA-D-GLUCOPYRANOSYL]OXY}METHYL)-4-HYDROXY-1-{[(15-METHYLHEXADECANOYL)OXY]METHYL}-4-OXIDO-7-OXO-3,5-DIOXA-8-AZA-4-PHOSPHAHEPTACOS-1-YL 15-METHYLHEXADECANOATE
ChEMBL
DrugBank
ZINC
PDB chain6smq Chain A Residue 601 [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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PDB6smq Structural and functional insights into oligopeptide acquisition by the RagAB transporter from Porphyromonas gingivalis.
Resolution3.3 Å
Binding residue
(original residue number in PDB)
H543 Y545
Binding residue
(residue number reindexed from 1)
H429 Y431
Annotation score1
Enzymatic activity
Enzyme Commision number ?
Gene Ontology
Cellular Component
GO:0009279 cell outer membrane

View graph for
Cellular Component
External links
PDB RCSB:6smq, PDBe:6smq, PDBj:6smq
PDBsum6smq
PubMed32393857
UniProtQ7MXJ7

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