Protein profile

VK055_1812

dipeptide permease D

Genome: KpATCC43816

Gene: AIK80424.1 dtpD Structure source: AlphaFold + ColabFold UniProt A0A0H3GQ97
Amino acids 492
Annotations 11
Features 65
PDB binders 14
Druggability 0.985

Overview

Basic information about this protein and its source genome.

Accession
VK055_1812
Gene
AIK80424.1 dtpD
Status
annotated
Amino acids
492
Structure source
AlphaFold + ColabFold

Target profile

Computed evidence for target prioritization.

Human off-target
hit
Human identity (%)
32.692
Human E-value
5.600000000000001e-23
Gut microbiome off-target
hit
Essential (DEG)
N
DEG identity (%)
29.004
Localization
CytoplasmicMembrane
ColabFold pLDDT
87.3

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 0.985
Structure A0A0H3GQ97
Pocket Pocket 2
P2Rank 0.952
Structure A0A0H3GQ97
Pocket Pocket 1
ColabFold model
FPocket 0.727 · Pocket 31
P2Rank 0.953 · Pocket 1
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 42 / 4744 genomes with a hit
Normalized 0.009

Sequence

Primary amino-acid sequence viewer.

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

11 GO

Gene Ontology (GO)

11
  • GO:1904680 Enables the transfer of a peptide from one side of a membrane to the other.
  • 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:0006857 The directed movement of oligopeptides into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. Oligopeptides are molecules that contain a small number (2 to 20) of amino-acid residues connected by peptide linkages.
  • GO:0015833 The directed movement of peptides, compounds of two or more amino acids where the alpha carboxyl group of one is bound to the alpha amino group of another, into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
  • 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:0042938 The directed movement of a dipeptide, a combination of two amino acids by means of a peptide (-CO-NH-) link, into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
  • GO:0071916 Enables the transfer of a dipeptide from one side of a membrane to the other. A dipeptide is a combination of two amino acids linked together by a peptide (-CO-NH-) bond.
  • GO:0015333 Enables the transfer of a solute or solutes from one side of a membrane to the other according to the reaction: peptide(out) + H+(out) = peptide(in) + H+(in), up its concentration gradient. The transporter binds the solute and undergoes a series of conformational changes. Transport works equally well in either direction and is driven by hydrogen ion movement.
  • GO:0015031 The directed movement of proteins into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.

Sequence Features

Domain/signature hits from InterPro and related databases.

65 records
Show feature table
Start End DB Term Name
311 332 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
188 207 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm.
366 376 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
410 432 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
140 152 ProSitePatterns PS01023 PTR2 family proton/oligopeptide symporters signature 2.
140 152 InterPro IPR018456 PTR2 family proton/oligopeptide symporter, conserved site
65 89 ProSitePatterns PS01022 PTR2 family proton/oligopeptide symporters signature 1.
65 89 InterPro IPR018456 PTR2 family proton/oligopeptide symporter, conserved site
13 35 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
48 69 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
45 67 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
1 492 FunFam G3DSA:1.20.1250.20:FF:000035 Dipeptide permease D
410 434 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
12 36 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
8 477 CDD cd17346 MFS_DtpA_like
8 477 InterPro IPR005279 Dipeptide/tripeptide permease
138 162 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
77 443 Pfam PF00854 POT family
77 443 InterPro IPR000109 Proton-dependent oligopeptide transporter family
167 189 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
232 236 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
10 483 ProSiteProfiles PS50850 Major facilitator superfamily (MFS) profile.
10 483 InterPro IPR020846 Major facilitator superfamily domain
5 189 SUPERFAMILY SSF103473 MFS general substrate transporter
5 189 InterPro IPR036259 MFS transporter superfamily
70 75 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm.
101 117 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
344 365 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
399 409 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm.
454 479 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
98 117 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
1 492 Gene3D G3DSA:1.20.1250.20 MFS general substrate transporter like domains
1 492 InterPro IPR036259 MFS transporter superfamily
72 94 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
168 187 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
344 366 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
480 492 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm.
376 398 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
285 310 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
377 398 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
267 284 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
256 266 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm.
210 232 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
208 231 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
237 255 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
435 453 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
96 100 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
118 137 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm.
2 483 PANTHER PTHR23517 RESISTANCE PROTEIN MDTM, PUTATIVE-RELATED-RELATED
163 167 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
37 47 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
333 343 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm.
76 95 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
208 480 SUPERFAMILY SSF103473 MFS general substrate transporter
208 480 InterPro IPR036259 MFS transporter superfamily
1 492 Hamap MF_01880 Dipeptide permease D [dtpD].
1 492 InterPro IPR023777 Amino acid/peptide transporter family, dipeptide permease D
269 288 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
457 479 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
237 256 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
310 332 TMHMM TMhelix 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.
138 157 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
6 464 NCBIfam TIGR00924 oligopeptide:H+ symporter
6 464 InterPro IPR005279 Dipeptide/tripeptide permease

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_A0A0H3GQ97
AlphaFold full sequence Viewing
ColabFold VK055_1812
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
2 0.985
36 0.296

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 27.43 0.92
2 8.01 0.426
3 2.05 0.045
4 2.02 0.044
5 1.89 0.038

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.

64 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
78M Q5M4H8 314.5 Da LogP 3.75 TPSA 66.8 ✓ Ro5 ✓ Clean CCCCCCC/C=C\CCCCCC(=O)OC[C@H](CO)O
78N Q5M4H8 314.5 Da LogP 3.75 TPSA 66.8 ✓ Ro5 ✓ Clean CCCCCCC/C=C\CCCCCC(=O)OC[C@@H](CO)O
97M Q5M4H8 328.5 Da LogP 4.14 TPSA 66.8 ✓ Ro5 ✓ Clean CCCCCC/C=C\CCCCCCCC(=O)OC[C@@H](CO)O
97N Q5M4H8 328.5 Da LogP 4.14 TPSA 66.8 ✓ Ro5 ✓ Clean CCCCCC/C=C\CCCCCCCC(=O)OC[C@H](CO)O
AFS Q8EHE6 196.1 Da LogP -1.03 TPSA 112.7 ✓ Ro5 ✓ Clean C[C@@H](C(=O)N[C@@H](C)P(=O)(O)O)N
F9E P77304 354.4 Da LogP -1.44 TPSA 171.4 ✓ Ro5 ✓ Clean CC(C)[C@@H](C(=O)OC[C@H](CO)OCn1cnc2c1NC(=NC2=O…
LMT P77304 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…
OLA Q5KYD1 282.5 Da LogP 6.11 TPSA 37.3 1 viol. ✓ Clean CCCCCCCC\C=C/CCCCCCCC(=O)O
OLB Q5KYD1 356.5 Da LogP 4.92 TPSA 66.8 ✓ Ro5 ✓ Clean CCCCCCCC/C=C\CCCCCCCC(=O)OC[C@H](CO)O
OLC Q5KYD1 356.5 Da LogP 4.92 TPSA 66.8 ✓ Ro5 ✓ Clean CCCCCCCC\C=C/CCCCCCCC(=O)OC[C@@H](CO)O
OPK A0A2R9TD79 424.5 Da LogP 1.54 TPSA 173.9 ✓ Ro5 ✓ Clean CC(C)[C@@H](C(=O)O)NC(=O)[C@H](CCCCNC(=O)OCc1cc…
PE5 Q5M4H8 398.5 Da LogP 0.13 TPSA 94.1 ✓ Ro5 ✓ Clean CCOCCOCCOCCOCCOCCOCCOCCOCCO
PG0 Q5M4H8 120.1 Da LogP -0.36 TPSA 38.7 ✓ Ro5 ✓ Clean COCCOCCO
UMQ A0A2R9TD79 496.6 Da LogP -0.84 TPSA 178.5 2 viol. ✓ Clean CCCCCCCCCCCO[C@H]1[C@@H]([C@H]([C@@H]([C@H](O1)…

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.