Protein profile

VK055_2106

acrB RND-type permease

Genome: KpATCC43816

Gene: AIK80711.1 acrB Structure source: Experimental + ColabFold UniProt W9B4M6
Amino acids 1048
Annotations 8
Features 85
PDB binders 34
Druggability 0.997

Overview

Basic information about this protein and its source genome.

Accession
VK055_2106
Gene
AIK80711.1 acrB
Status
annotated
Amino acids
1048
Structure source
Experimental + ColabFold

Target profile

Computed evidence for target prioritization.

Human off-target
No hit
Human identity (%)
0.0
Gut microbiome off-target
hit
Essential (DEG)
Y
DEG identity (%)
92.088
DEG E-value
0.0
Localization
CytoplasmicMembrane
ColabFold pLDDT
90.93

Selected Druggability evidence

PDB experimental structure

Selected Druggability is the FPocket score chosen for ranking using the curated structure priority. The 3D viewer may show a different loaded structure, so its visible pockets can differ.

FPocket 0.997
Structure 8FFS
Pocket Pocket 1
P2Rank 0.942
Structure 8FFS
Pocket Pocket 1
ColabFold model
FPocket 0.951 · Pocket 58
P2Rank 0.968 · Pocket 1
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 273 / 4744 genomes with a hit
Normalized 0.058

Sequence

Primary amino-acid sequence viewer.

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

8 GO

Gene Ontology (GO)

8
  • GO:0016020 A lipid bilayer along with all the proteins and protein complexes embedded in it and attached to it.
  • GO:0055085 The process in which a solute is transported across a lipid bilayer, from one side of a membrane to the other.
  • GO:0022857 Enables the transfer of a substance, usually a specific substance or a group of related substances, from one side of a membrane to the other.
  • GO:0042908 The directed movement of a xenobiotic into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. A xenobiotic is a compound foreign to the organism exposed to it. It may be synthesized by another organism (like ampicilin) or it can be a synthetic chemical.
  • GO:0015562 Enables the transfer of a specific substance or related group of substances from the inside of the cell to the outside of the cell across a membrane.
  • GO:0005886 The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.
  • GO:0042910 Enables the directed movement of a xenobiotic from one side of a membrane to the other. A xenobiotic is a compound foreign to the organism exposed to it. It may be synthesized by another organism (like ampicilin) or it can be a synthetic chemical.
  • GO:0009636 Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a toxic stimulus.

Sequence Features

Domain/signature hits from InterPro and related databases.

85 records
Show feature table
Start End DB Term Name
459 469 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
571 672 FunFam G3DSA:3.30.70.1430:FF:000002 Efflux pump membrane transporter
33 339 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
340 359 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
38 822 Gene3D G3DSA:3.30.70.1430 Multidrug efflux transporter AcrB pore domain
182 271 SUPERFAMILY SSF82714 Multidrug efflux transporter AcrB TolC docking domain; DN and DC subdomains
182 271 InterPro IPR027463 Multidrug efflux transporter AcrB TolC docking domain, DN/DC subdomains
872 891 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
296 497 SUPERFAMILY SSF82866 Multidrug efflux transporter AcrB transmembrane domain
396 416 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
360 365 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm.
180 278 Gene3D G3DSA:3.30.2090.10 Multidrug efflux transporter AcrB TolC docking domain; DN and DC subdomains
180 278 InterPro IPR027463 Multidrug efflux transporter AcrB TolC docking domain, DN/DC subdomains
10 32 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
874 891 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
1006 1028 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
2 1036 PANTHER PTHR32063 -
2 1036 InterPro IPR001036 Acriflavin resistance protein
38 133 SUPERFAMILY SSF82693 Multidrug efflux transporter AcrB pore domain; PN1, PN2, PC1 and PC2 subdomains
892 897 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm.
974 996 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
857 1025 FunFam G3DSA:1.20.1640.10:FF:000002 Efflux pump membrane transporter
724 811 SUPERFAMILY SSF82714 Multidrug efflux transporter AcrB TolC docking domain; DN and DC subdomains
724 811 InterPro IPR027463 Multidrug efflux transporter AcrB TolC docking domain, DN/DC subdomains
340 359 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
925 947 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
437 458 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
919 923 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
898 918 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
946 973 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm.
566 670 SUPERFAMILY SSF82693 Multidrug efflux transporter AcrB pore domain; PN1, PN2, PC1 and PC2 subdomains
391 395 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
366 390 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
726 814 Gene3D G3DSA:3.30.2090.10 Multidrug efflux transporter AcrB TolC docking domain; DN and DC subdomains
726 814 InterPro IPR027463 Multidrug efflux transporter AcrB TolC docking domain, DN/DC subdomains
133 331 Gene3D G3DSA:3.30.70.1320 Multidrug efflux transporter AcrB pore domain like
369 391 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
417 436 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm.
557 873 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
726 814 FunFam G3DSA:3.30.2090.10:FF:000002 Efflux pump membrane transporter
540 556 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
974 994 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
1029 1048 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm.
517 1025 Gene3D G3DSA:1.20.1640.10 Multidrug efflux transporter AcrB transmembrane domain
38 138 FunFam G3DSA:3.30.70.1430:FF:000001 Efflux pump membrane transporter
1 1029 Pfam PF00873 AcrB/AcrD/AcrF family
1 1029 InterPro IPR001036 Acriflavin resistance protein
180 278 FunFam G3DSA:3.30.2090.10:FF:000001 Efflux pump membrane transporter
995 1005 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
1 1048 NCBIfam TIGR00915 efflux RND transporter permease subunit
1 1048 InterPro IPR004764 Multidrug resistance protein MdtF-like
135 330 SUPERFAMILY SSF82693 Multidrug efflux transporter AcrB pore domain; PN1, PN2, PC1 and PC2 subdomains
7 516 Gene3D G3DSA:1.20.1640.10 Multidrug efflux transporter AcrB transmembrane domain
470 492 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
12 32 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
322 509 FunFam G3DSA:1.20.1640.10:FF:000001 Efflux pump membrane transporter
438 460 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
470 494 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
540 557 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
898 920 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
495 539 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm.
924 945 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
808 1034 SUPERFAMILY SSF82866 Multidrug efflux transporter AcrB transmembrane domain
571 672 Gene3D G3DSA:3.30.70.1430 Multidrug efflux transporter AcrB pore domain
1006 1028 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
1 11 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm.
673 872 Gene3D G3DSA:3.30.70.1440 Multidrug efflux transporter AcrB pore domain
553 570 PRINTS PR00702 Acriflavin resistance protein family signature
553 570 InterPro IPR001036 Acriflavin resistance protein
445 468 PRINTS PR00702 Acriflavin resistance protein family signature
445 468 InterPro IPR001036 Acriflavin resistance protein
36 54 PRINTS PR00702 Acriflavin resistance protein family signature
36 54 InterPro IPR001036 Acriflavin resistance protein
336 359 PRINTS PR00702 Acriflavin resistance protein family signature
336 359 InterPro IPR001036 Acriflavin resistance protein
363 384 PRINTS PR00702 Acriflavin resistance protein family signature
363 384 InterPro IPR001036 Acriflavin resistance protein
470 493 PRINTS PR00702 Acriflavin resistance protein family signature
470 493 InterPro IPR001036 Acriflavin resistance protein
391 415 PRINTS PR00702 Acriflavin resistance protein family signature
391 415 InterPro IPR001036 Acriflavin resistance protein
622 636 PRINTS PR00702 Acriflavin resistance protein family signature
622 636 InterPro IPR001036 Acriflavin resistance protein
8 32 PRINTS PR00702 Acriflavin resistance protein family signature
8 32 InterPro IPR001036 Acriflavin resistance protein

3D Structure

Selected loaded structure. Experimental PDB entries may cover only a portion of the sequence; predicted models typically cover the full protein.

3D visualization script Full viewer

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Structural evidence

1 + 1

Experimental PDB entries and predicted models. Click Switch to display a different structure in the viewer.

Entry Method Resolution Chain Coverage Links Status
PDB 8FFS
X-ray 20.00 Å - Viewing
ColabFold VK055_2106
ColabFold full sequence Loaded
Pocket details FPocket · P2Rank — toggle visibility and zoom from here, or open full viewer

Pockets (FPOCKET)

Showing top-ranked FPocket candidates by druggability. Druggability is color-coded: high (0.7 or higher), medium (0.4 to 0.69), low (below 0.4).

FPOCKET Sticks Spheres Surfaces Druggability Labels Zoom Positions
199 0.999
1 0.997
159 0.994

Pockets (P2RANK)

Showing top-ranked P2Rank candidates by probability. Probability is color-coded per P2Rank calibration: high (≥ 0.5), medium (0.2 – 0.49), low (< 0.2).

P2RANK Sticks Spheres Surfaces Score Probability Labels Zoom Positions
1 32.26 0.942
2 17.36 0.801
3 15.33 0.751
4 14.55 0.726
5 14.27 0.717

Ligand evidence

Ligands grouped by evidence source. PDB ligands keep the source crystal visible, and loaded crystals can be opened directly in the structure viewer.

137 records

Structural evidence inferred from similar proteins. The source crystal indicates where the ligand was observed; the UniProt column identifies the homologous protein carrying that ligand.

Show only:
Ligand Source crystal UniProt (homolog) MW · LogP · TPSA Lipinski PAINS SMILES
3PE Q2FD94 748.1 Da LogP 12.06 TPSA 134.4 2 viol. ✓ Clean CCCCCCCCCCCCCCCCCC(=O)OC[C@H](COP(=O)(O)OCCN)OC…
3YI P31224 725.8 Da LogP 4.57 TPSA 218.4 3 viol. Alert Cc1c(c2c3c4c1O[C@@](C4=O)(O/C=C/[C@@H]([C@H]([C…
5QF P31224 526.7 Da LogP 3.92 TPSA 80.1 1 viol. ✓ Clean CC1(Cc2c(c(nc(c2C#N)SCCc3ccc(c(c3)OC)OC)N4CCN(C…
8K6 P31224 254.5 Da LogP 7.27 TPSA 0.0 1 viol. ✓ Clean CCCCCCCCCCCCCCCCCC
AIC P31224 349.4 Da LogP 0.32 TPSA 112.7 ✓ Ro5 ✓ Clean CC1([C@@H](N2[C@H](S1)[C@@H](C2=O)NC(=O)[C@@H](…
AIX Q5F725 351.4 Da LogP 0.26 TPSA 121.5 ✓ Ro5 ✓ Clean CC1([C@@H](N[C@H](S1)[C@@H](C=O)NC(=O)[C@@H](c2…
AV0 P52002 1005.2 Da LogP -1.68 TPSA 357.1 3 viol. ✓ Clean CCCCCCCCCCC(CCCCCCCCCC)(CO[C@H]1[C@@H]([C@H]([C…
C14 P31224 198.4 Da LogP 5.71 TPSA 0.0 1 viol. ✓ Clean CCCCCCCCCCCCCC
D10 P31224 142.3 Da LogP 4.15 TPSA 0.0 ✓ Ro5 ✓ Clean CCCCCCCCCC
D12 P31224 170.3 Da LogP 4.93 TPSA 0.0 ✓ Ro5 ✓ Clean CCCCCCCCCCCC
DD9 P31224 128.3 Da LogP 3.76 TPSA 0.0 ✓ Ro5 ✓ Clean CCCCCCCCC
DDQ P31224 201.4 Da LogP 3.70 TPSA 23.1 ✓ Ro5 ✓ Clean CCCCCCCCCC[N+](C)(C)[O-]
DDR P31224 400.6 Da LogP 5.72 TPSA 72.8 1 viol. ✓ Clean CCCCCCCCCC(=O)OC[C@H](CO)OC(=O)CCCCCCCCC
DM2 P31224 543.5 Da LogP 0.00 TPSA 206.1 3 viol. Alert C[C@H]1[C@H]([C@H](C[C@@H](O1)O[C@H]2C[C@@](Cc3…
ERY P31224 733.9 Da LogP 1.79 TPSA 193.9 2 viol. ✓ Clean CC[C@@H]1[C@@]([C@@H]([C@H](C(=O)[C@@H](C[C@@](…
ET Q2FD70 314.4 Da LogP 4.13 TPSA 55.9 ✓ Ro5 Alert CC[n+]1c2cc(ccc2c3ccc(cc3c1c4ccccc4)N)N
ETE P31224 208.3 Da LogP -0.33 TPSA 57.2 ✓ Ro5 ✓ Clean COCCOCCOCCOCCO
FUA P31224 516.7 Da LogP 5.67 TPSA 104.1 2 viol. ✓ Clean C[C@H]1[C@@H]2CC[C@]3([C@H]([C@]2(CC[C@H]1O)C)[…
HEX P31224 86.2 Da LogP 2.59 TPSA 0.0 ✓ Ro5 ✓ Clean CCCCCC
LMT P31224 510.6 Da LogP -0.45 TPSA 178.5 3 viol. ✓ Clean CCCCCCCCCCCCO[C@H]1[C@@H]([C@H]([C@@H]([C@H](O1…
LMU P31224 510.6 Da LogP -0.45 TPSA 178.5 3 viol. ✓ Clean CCCCCCCCCCCCO[C@@H]1[C@@H]([C@H]([C@@H]([C@H](O…
LPX P31224 453.6 Da LogP 4.46 TPSA 128.3 ✓ Ro5 ✓ Clean CCCCCCCCCCCCCCCC(=O)OC[C@@H](CO[P@](=O)(O)OCCN)O
MIY P31224 457.5 Da LogP 0.19 TPSA 164.6 ✓ Ro5 ✓ Clean CN(C)c1ccc(c2c1C[C@H]3C[C@H]4[C@@H](C(=C(C(=O)[…
MYS P31224 212.4 Da LogP 6.10 TPSA 0.0 1 viol. ✓ Clean CCCCCCCCCCCCCCC
OCT P31224 114.2 Da LogP 3.37 TPSA 0.0 ✓ Ro5 ✓ Clean CCCCCCCC
P3G P31224 250.3 Da LogP 1.11 TPSA 46.2 ✓ Ro5 ✓ Clean CCOCCOCCOCCOCCOCC
P9D P31224 693.8 Da LogP 0.91 TPSA 212.5 2 viol. ✓ Clean CC(C)(C)c1csc(n1)NC(=O)C2=CC3=NC(=C(C(=O)N3C=C2…
PTY P31224 734.1 Da LogP 11.67 TPSA 134.4 2 viol. ✓ Clean CCCCCCCCCCCCCCCCCCCC(=O)O[C@H](COC(=O)CCCCCCCCC…
PUY P31224 471.5 Da LogP -0.79 TPSA 160.9 1 viol. ✓ Clean CN(C)c1c2c(ncn1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H]…
R16 P31224 226.4 Da LogP 6.49 TPSA 0.0 1 viol. ✓ Clean CCCCCCCCCCCCCCCC
RBT P31224 847.0 Da LogP 4.62 TPSA 205.5 2 viol. Alert Cc1c(c2c3c4c1O[C@@](C4=O)(O\C=C\[C@@H]([C@H]([C…
RFP P31224 823.0 Da LogP 4.34 TPSA 220.1 3 viol. Alert Cc1c(c2c3c4c1O[C@@](C4=O)(O\C=C\[C@@H]([C@H]([C…
XPE P31224 458.5 Da LogP -0.88 TPSA 123.5 1 viol. ✓ Clean C(COCCOCCOCCOCCOCCOCCOCCOCCOCCO)O
YQM Q2FD94 558.6 Da LogP 0.14 TPSA 193.7 2 viol. ✓ Clean CN(C)[C@H]1[C@@H]2C[C@@H]3Cc4c(cc(c(c4C(=C3C(=O…

PDB and ChEMBL records on this protein are shown in full. ChEMBL records from similar proteins are capped at the top 100 per protein (by pchembl) and ZINC at the top 50 (Tanimoto ≥ 0.5). ADME columns are descriptor-based screening flags, not experimental toxicity results.