Protein profile

KP13_05076

Multidrug efflux pump KexD

Genome: KpKP13

Gene: AHE44193.1 kexD Structure source: AlphaFold + ColabFold UniProt A0A0H3GUM9
Amino acids 1038
Annotations 8
Features 87
PDB binders 34
Druggability 0.911

Overview

Basic information about this protein and its source genome.

Accession
KP13_05076
Gene
AHE44193.1 kexD
Status
annotated
Amino acids
1038
Structure source
AlphaFold + 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 (%)
52.381
DEG E-value
0.0
Localization
CytoplasmicMembrane
ColabFold pLDDT
89.68

Selected Druggability evidence

AlphaFold / UniProt model

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 0.911
Structure A0A0H3GUM9
Pocket Pocket 8
P2Rank 0.987
Structure A0A0H3GUM9
Pocket Pocket 1
ColabFold model
FPocket 0.383 · Pocket 55
P2Rank 0.978 · Pocket 1
Core conservation Accessory gene
Roary accessory
CoreCruncher accessory
Gut microbiome 51 / 4744 genomes with a hit
Normalized 0.011

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: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: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: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: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: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.

87 records
Show feature table
Start End DB Term Name
541 562 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
540 562 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
5 27 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
922 941 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
133 331 Gene3D G3DSA:3.30.70.1320 Multidrug efflux transporter AcrB pore domain like
366 386 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
563 865 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
38 139 FunFam G3DSA:3.30.70.1430:FF:000001 Efflux pump membrane transporter
918 942 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
22 26 Phobius SIGNAL_PEPTIDE_C_REGION C-terminal region of a signal peptide.
445 468 PRINTS PR00702 Acriflavin resistance protein family signature
445 468 InterPro IPR001036 Acriflavin resistance protein
363 384 PRINTS PR00702 Acriflavin resistance protein family signature
363 384 InterPro IPR001036 Acriflavin resistance protein
552 569 PRINTS PR00702 Acriflavin resistance protein family signature
552 569 InterPro IPR001036 Acriflavin resistance protein
8 32 PRINTS PR00702 Acriflavin resistance protein family signature
8 32 InterPro IPR001036 Acriflavin resistance protein
619 633 PRINTS PR00702 Acriflavin resistance protein family signature
619 633 InterPro IPR001036 Acriflavin resistance protein
391 415 PRINTS PR00702 Acriflavin resistance protein family signature
391 415 InterPro IPR001036 Acriflavin resistance protein
336 359 PRINTS PR00702 Acriflavin resistance protein family signature
336 359 InterPro IPR001036 Acriflavin resistance protein
36 54 PRINTS PR00702 Acriflavin resistance protein family signature
36 54 InterPro IPR001036 Acriflavin resistance protein
470 493 PRINTS PR00702 Acriflavin resistance protein family signature
470 493 InterPro IPR001036 Acriflavin resistance protein
135 329 SUPERFAMILY SSF82693 Multidrug efflux transporter AcrB pore domain; PN1, PN2, PC1 and PC2 subdomains
434 458 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
721 803 SUPERFAMILY SSF82714 Multidrug efflux transporter AcrB TolC docking domain; DN and DC subdomains
721 803 InterPro IPR027463 Multidrug efflux transporter AcrB TolC docking domain, DN/DC subdomains
565 665 SUPERFAMILY SSF82693 Multidrug efflux transporter AcrB pore domain; PN1, PN2, PC1 and PC2 subdomains
296 497 SUPERFAMILY SSF82866 Multidrug efflux transporter AcrB transmembrane domain
183 271 SUPERFAMILY SSF82714 Multidrug efflux transporter AcrB TolC docking domain; DN and DC subdomains
183 271 InterPro IPR027463 Multidrug efflux transporter AcrB TolC docking domain, DN/DC subdomains
337 359 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
962 984 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
414 433 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm.
892 912 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
340 359 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
835 1021 SUPERFAMILY SSF82866 Multidrug efflux transporter AcrB transmembrane domain
1 26 Phobius SIGNAL_PEPTIDE Signal peptide region
863 885 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
38 816 Gene3D G3DSA:3.30.70.1430 Multidrug efflux transporter AcrB pore domain
988 998 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
438 460 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
1 9 Phobius SIGNAL_PEPTIDE_N_REGION N-terminal region of a signal peptide.
7 515 Gene3D G3DSA:1.20.1640.10 Multidrug efflux transporter AcrB transmembrane domain
913 917 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
10 21 Phobius SIGNAL_PEPTIDE_H_REGION Hydrophobic region of a signal peptide.
392 413 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
967 987 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
1 1021 Pfam PF00873 AcrB/AcrD/AcrF family
1 1021 InterPro IPR001036 Acriflavin resistance protein
999 1021 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
1022 1038 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm.
360 365 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm.
886 891 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm.
943 966 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm.
38 130 SUPERFAMILY SSF82693 Multidrug efflux transporter AcrB pore domain; PN1, PN2, PC1 and PC2 subdomains
313 509 FunFam G3DSA:1.20.1640.10:FF:000001 Efflux pump membrane transporter
890 912 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
470 497 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
475 497 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
2 1026 PANTHER PTHR32063 -
2 1026 InterPro IPR001036 Acriflavin resistance protein
498 540 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm.
720 808 Gene3D G3DSA:3.30.2090.10 Multidrug efflux transporter AcrB TolC docking domain; DN and DC subdomains
720 808 InterPro IPR027463 Multidrug efflux transporter AcrB TolC docking domain, DN/DC subdomains
866 885 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
392 414 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
570 667 Gene3D G3DSA:3.30.70.1430 Multidrug efflux transporter AcrB pore domain
668 852 SUPERFAMILY SSF82693 Multidrug efflux transporter AcrB pore domain; PN1, PN2, PC1 and PC2 subdomains
387 391 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
668 866 Gene3D G3DSA:3.30.70.1440 Multidrug efflux transporter AcrB pore domain
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
516 1018 Gene3D G3DSA:1.20.1640.10 Multidrug efflux transporter AcrB transmembrane domain
366 388 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
459 469 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
999 1021 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
400 495 ProSiteProfiles PS50156 Sterol-sensing domain (SSD) profile.
400 495 InterPro IPR000731 Sterol-sensing domain
1 1027 NCBIfam TIGR00915 efflux RND transporter permease subunit
1 1027 InterPro IPR004764 Multidrug resistance protein MdtF-like
27 336 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.

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

0 + 2

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

Entry Method Resolution Chain Coverage Links Status
AlphaFold AF_A0A0H3GUM9
AlphaFold full sequence Viewing
ColabFold KP13_05076
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
8 0.911
68 0.674
21 0.668
12 0.23

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 21.75 0.874
2 10.48 0.563
3 8.93 0.478
4 5.1 0.233
5 3.14 0.106

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 P52002 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 Q2FD70 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.