Structure of PDB 8f4r Chain B Binding Site BS01

Receptor Information

>8f4r Chain B (length=1033) Species: 562 (Escherichia coli)

MANFFIDRPIFAWVLAILLCLTGTLAIFSLPVEQYPDLAPPNVRVTANYP
GASAQTLENTVTQVIEQNMTGLDNLMYMSSQSSGTGQASVTLSFKAGTDP
DEAVQQVQNQLQSAMRKLPQAVQNQGVTVRKTGDTNILTIAFVSTDGSMD
KQDIADYVASNIQDPLSRVNGVGDIDAYGSQYSMRIWLDPAKLNSFQMTA
KDVTDAIESQNAQIAVGQLGGTPSVDKQALNATINAQSLLQTPEQFRDIT
LRVNQDGSEVRLGDVATVEMGAEKYDYLSRFNGKPASGLGVKLASGANEM
ATAELVLNRLDELAQYFPHGLEYKVAYETTSFVKASIEDVVKTLLEAIAL
VFLVMYLFLQNFRATLIPTIAVPVVLMGTFSVLYAFGYSVNTLTMFAMVL
AIGLLVDDAIVVVENVERIMSEEGLTPREATRKSMGQIQGALVGIAMVLS
AVFVPMAFFGGTTGAIYRQFSITIVAAMVLSVLVAMILTPALCATLLKPL
KKGEHHGQKGFFAWFNQMFNRNAERYEKGVAKILHRSLRWIVIYVLLLGG
MVFLFLRLPTSFLPLEDRGMFTTSVQLPSGSTQQQTLKVVEQIEKYYFTH
EKDNIMSVFATVGSGPGGNGQNVARMFIRLKDWSERDSKTGTSFAIIERA
TKAFNQIKEARVIASSPPAISGLGSSAGFDMELQDHAGAGHDALMAARNQ
LLALAAENPELTRVRHNGLDDSPQLQIDIDQRKAQALGVAIDDINDTLQT
AWGSSYVNDFMDRGRVKKVYVQAAAPYRMLPDDINLWYVRNKDGGMVPFS
AFATSRWETGSPRLERYNGYSAVEIVGEAAPGVSTGTAMDIMESLVKQLP
NGFGLEWTAMSYQERLSGAQAPALYAISLLVVFLCLAALYESWSVPFSVM
LVVPLGVIGALLATWMRGLENDVYFQVGLLTVIGLSAKNAILIVEFANEM
NQKGHDLFEATLHACRQRLRPILMTSLAFIFGVLPMATSTGAGSGGQHAV
GTGVMGGMISATILAIYFVPLFFVLVRRRFPLK

Ligand information

• Ligand ID: LLL
• InChI: InChI=1S/C19H39N5O7/c1-19(27)7-28-18(13(26)16(19)24-2)31-15-11(23)5-10(22)14(12(15)25)30-17-9(21)4-3-8(6-20)29-17/h8-18,24-27H,3-7,20-23H2,1-2H3/t8-,9+,10-,11+,12-,13+,14+,15-,16+,17+,18+,19-/m0/s1
• InChIKey: VEGXETMJINRLTH-BOZYPMBZSA-N
• SMILES:
  CACTVS 3.341: CN[CH]1[CH](O)[CH](OC[C]1(C)O)O[CH]2[CH](N)C[CH](N)[CH](O[CH]3O[CH](CN)CC[CH]3N)[CH]2O
  ACDLabs 10.04: O(C2C(O)C(OC1OC(CN)CCC1N)C(N)CC2N)C3OCC(O)(C(NC)C3O)C
  OpenEye OEToolkits 1.5.0: CC1(COC(C(C1NC)O)OC2C(CC(C(C2O)OC3C(CCC(O3)CN)N)N)N)O
  OpenEye OEToolkits 1.5.0: C[C@@]1(CO[C@@H]([C@@H]([C@H]1NC)O)O[C@H]2[C@@H](C[C@@H]([C@H]([C@@H]2O)O[C@@H]3[C@@H](CC[C@H](O3)CN)N)N)N)O
  CACTVS 3.341: CN[C@@H]1[C@@H](O)[C@H](OC[C@]1(C)O)O[C@H]2[C@H](N)C[C@H](N)[C@@H](O[C@H]3O[C@H](CN)CC[C@H]3N)[C@@H]2O
• Formula: C19 H39 N5 O7
• Name: (2R,3R,4R,5R)-2-((1S,2S,3R,4S,6R)-4,6-DIAMINO-3-((2R,3R,6S)-3-AMINO-6-(AMINOMETHYL)-TETRAHYDRO-2H-PYRAN-2-YLOXY)-2-HYDR OXYCYCLOHEXYLOXY)-5-METHYL-4-(METHYLAMINO)-TETRAHYDRO-2H-PYRAN-3,5-DIOL;
  GENTAMICIN C1A
• ChEMBL: CHEMBL194126
• DrugBank: DB04729
• ZINC: ZINC000008216590
• PDB chain: 8f4r Chain B Residue 1101

Receptor-Ligand Complex Structure

Structure summary

• PDB: 8f4r Cryo-EM Structures of AcrD Illuminate a Mechanism for Capturing Aminoglycosides from Its Central Cavity.
• Resolution: 3.06 Å
• Binding residue (original residue number in PDB): D99 D101 E102
• Binding residue (residue number reindexed from 1): D99 D101 E102
• Annotation score: 1

Gene Ontology

Molecular Function

• GO:0005515 protein binding
• GO:0015125 bile acid transmembrane transporter activity
• GO:0015562 efflux transmembrane transporter activity
• GO:0022857 transmembrane transporter activity
• GO:0042910 xenobiotic transmembrane transporter activity

Biological Process

• GO:0009636 response to toxic substance
• GO:0015721 bile acid and bile salt transport
• GO:0042908 xenobiotic transport
• GO:0046677 response to antibiotic
• GO:0055085 transmembrane transport
• GO:0140330 xenobiotic detoxification by transmembrane export across the cell outer membrane

Cellular Component

• GO:0005886 plasma membrane
• GO:0016020 membrane
• GO:0098567 periplasmic side of plasma membrane
• GO:1990281 efflux pump complex

External links

• PDB: RCSB:8f4r, PDBe:8f4r, PDBj:8f4r
• PDBsum: 8f4r
• PubMed: 36625574
• UniProt: P24177|ACRD_ECOLI Probable aminoglycoside efflux pump (Gene Name=acrD)