Structure of PDB 4dx7 Chain B Binding Site BS01

Receptor Information

>4dx7 Chain B (length=1033) Species: 83333 (Escherichia coli K-12)

MPNFFIDRPIFAWVIAIIIMLAGGLAILKLPVAQYPTIAPPAVTISASYP
GADAKTVQDTVTQVIEQNMNGIDNLMYMSSNSDSTGTVQITLTFESGTDA
DIAQVQVQNKLQLAMPLLPQEVQQQGVSVEKSSSSFLMVVGVINTDGTMT
QEDISDYVAANMKDAISRTSGVGDVQLFGSQYAMRIWMNPNELNKFQLTP
VDVITAIKAQNAQVAAGQLGGTPPVKGQQLNASIIAQTRLTSTEEFGKIL
LKVNQDGSRVLLRDVAKIELGGENYDIIAEFNGQPASGLGIKLATGANAL
DTAAAIRAELAKMEPFFPSGLKIVYPYDTTPFVKISIHEVVKTLVEAIIL
VFLVMYLFLQNFRATLIPTIAVPVVLLGTFAVLAAFGFSINTLTMFGMVL
AIGLLVDDAIVVVENVERVMAEEGLPPKEATRKSMGQIQGALVGIAMVLS
AVFVPMAFFGGSTGAIYRQFSITIVSAMALSVLVALILTPALCATMLKPI
AKGDHGEGKKGFFGWFNRMFEKSTHHYTDSVGGILRSTGRYLVLYLIIVV
GMAYLFVRLPSSFLPDEDQGVFMTMVQLPAGATQERTQKVLNEVTHYYLT
KEKNNVESVFAVNGFGFAGRGQNTGIAFVSLKDWADRPGEENKVEAITMR
ATRAFSQIKDAMVFAFNLPAIVELGTATGFDFELIDQAGLGHEKLTQARN
QLLAEAAKHPDMLTSVRPNGLEDTPQFKIDIDQEKAQALGVSINDINTTL
GAAWGGSYVNDFIDRGRVKKVYVMSEAKYRMLPDDIGDWYVRAADGQMVP
FSAFSSSRWEYGSPRLERYNGLPSMEILGQAAPGKSTGEAMELMEQLASK
LPTGVGYDWTGMSYQERLSGNQAPSLYAISLIVVFLCLAALYESWSIPFS
VMLVVPLGVIGALLAATFRGLTNDVYFQVGLLTTIGLSAKNAILIVEFAK
DLMDKEGKGLIEATLDAVRMRLRPILMTSLAFILGVMPLVISTGAGSGAQ
NAVGTGVMGGMVTATVLAIFFVPVFFVVVRRRF

Ligand information

• Ligand ID: DM2
• InChI: InChI=1S/C27H29NO11/c1-10-22(31)13(28)6-17(38-10)39-15-8-27(36,16(30)9-29)7-12-19(15)26(35)21-20(24(12)33)23(32)11-4-3-5-14(37-2)18(11)25(21)34/h3-5,10,13,15,17,22,29,31,33,35-36H,6-9,28H2,1-2H3/t10-,13-,15-,17-,22+,27-/m0/s1
• InChIKey: AOJJSUZBOXZQNB-TZSSRYMLSA-N
• SMILES:
  CACTVS 3.341: COc1cccc2C(=O)c3c(O)c4C[C@](O)(C[C@H](O[C@H]5C[C@H](N)[C@H](O)[C@H](C)O5)c4c(O)c3C(=O)c12)C(=O)CO
  OpenEye OEToolkits 1.5.0: CC1C(C(CC(O1)OC2CC(Cc3c2c(c4c(c3O)C(=O)c5cccc(c5C4=O)OC)O)(C(=O)CO)O)N)O
  ACDLabs 10.04: O=C2c1c(O)c5c(c(O)c1C(=O)c3cccc(OC)c23)CC(O)(C(=O)CO)CC5OC4OC(C(O)C(N)C4)C
  OpenEye OEToolkits 1.5.0: C[C@H]1[C@H]([C@H](C[C@@H](O1)O[C@H]2C[C@@](Cc3c2c(c4c(c3O)C(=O)c5cccc(c5C4=O)OC)O)(C(=O)CO)O)N)O
  CACTVS 3.341: COc1cccc2C(=O)c3c(O)c4C[C](O)(C[CH](O[CH]5C[CH](N)[CH](O)[CH](C)O5)c4c(O)c3C(=O)c12)C(=O)CO
• Formula: C27 H29 N O11
• Name: DOXORUBICIN;
  ADRIAMYCIN
• ChEMBL: CHEMBL53463
• DrugBank: DB00997
• ZINC: ZINC000003918087
• PDB chain: 4dx7 Chain B Residue 1104

Receptor-Ligand Complex Structure

Structure summary

• PDB: 4dx7 Transport of drugs by the multidrug transporter AcrB involves an access and a deep binding pocket that are separated by a switch-loop.
• Resolution: 2.253 Å
• Binding residue (original residue number in PDB): Q89 E130 Q176 F178 V612 F615
• Binding residue (residue number reindexed from 1): Q89 E130 Q176 F178 V612 F615
• 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:0015567 alkane transmembrane transporter activity
• GO:0022857 transmembrane transporter activity
• GO:0042802 identical protein binding
• GO:0042910 xenobiotic transmembrane transporter activity
• GO:0042931 enterobactin transmembrane transporter activity

Biological Process

• GO:0009410 response to xenobiotic stimulus
• GO:0009636 response to toxic substance
• GO:0015721 bile acid and bile salt transport
• GO:0015895 alkane transport
• GO:0015908 fatty acid transport
• GO:0042908 xenobiotic transport
• GO:0042930 enterobactin 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:4dx7, PDBe:4dx7, PDBj:4dx7
• PDBsum: 4dx7
• PubMed: 22451937
• UniProt: P31224|ACRB_ECOLI Multidrug efflux pump subunit AcrB (Gene Name=acrB)