Protein profile

VK055_1219

sodium:dicarboxylate symporter family protein

Genome: KpATCC43816

Gene: AIK79842.1 Structure source: ColabFold
Amino acids 386
Annotations 2
Features 43
PDB binders 12
Druggability 0.838

Overview

Basic information about this protein and its source genome.

Accession
VK055_1219
Gene
AIK79842.1
Status
annotated
Amino acids
386
Structure source
ColabFold

Target profile

Computed evidence for target prioritization.

Human off-target
hit
Human identity (%)
31.206
Human E-value
1.04e-07
Gut microbiome off-target
hit
Essential (DEG)
N
DEG identity (%)
31.25
Localization
CytoplasmicMembrane
ColabFold pLDDT
89.24

Selected Druggability evidence

ColabFold / curated 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 0.838
Structure CB_VK055_1219
Pocket Pocket 8
P2Rank 0.34
Structure CB_VK055_1219
Pocket Pocket 1
ColabFold model
FPocket 0.838 · Pocket 8
P2Rank 0.34 · Pocket 1
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 226 / 4744 genomes with a hit
Normalized 0.048

Sequence

Primary amino-acid sequence viewer.

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

2 GO

Gene Ontology (GO)

2
  • GO:0016020 A lipid bilayer along with all the proteins and protein complexes embedded in it and attached to it.
  • GO:0015293 Enables the active transport of a solute across a membrane by a mechanism whereby two or more species are transported together in the same direction in a tightly coupled process not directly linked to a form of energy other than chemiosmotic energy.

Sequence Features

Domain/signature hits from InterPro and related databases.

43 records
Show feature table
Start End DB Term Name
180 207 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
169 179 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
219 238 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
1 5 Phobius SIGNAL_PEPTIDE_N_REGION N-terminal region of a signal peptide.
313 317 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
1 366 SUPERFAMILY SSF118215 Proton glutamate symport protein
1 366 InterPro IPR036458 Sodium:dicarboxylate symporter superfamily
1 385 FunFam G3DSA:1.10.3860.10:FF:000004 L-cystine transporter tcyP
183 205 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
263 285 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
103 125 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
148 168 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
17 21 Phobius SIGNAL_PEPTIDE_C_REGION C-terminal region of a signal peptide.
293 312 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
1 21 Phobius SIGNAL_PEPTIDE Signal peptide region
208 218 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm.
258 281 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
77 95 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
129 147 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm.
318 338 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
1 385 Gene3D G3DSA:1.10.3860.10 Sodium:dicarboxylate symporter
1 385 InterPro IPR036458 Sodium:dicarboxylate symporter superfamily
6 16 Phobius SIGNAL_PEPTIDE_H_REGION Hydrophobic region of a signal peptide.
107 128 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
31 56 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
292 314 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
1 366 Pfam PF00375 Sodium:dicarboxylate symporter family
1 366 InterPro IPR001991 Sodium:dicarboxylate symporter
96 106 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
282 292 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm.
22 30 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
57 76 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm.
28 53 PRINTS PR00173 Glutamate-aspartate symporter signature
293 312 PRINTS PR00173 Glutamate-aspartate symporter signature
320 340 PRINTS PR00173 Glutamate-aspartate symporter signature
105 127 PRINTS PR00173 Glutamate-aspartate symporter signature
183 202 PRINTS PR00173 Glutamate-aspartate symporter signature
318 340 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
1 379 PANTHER PTHR42865 PROTON/GLUTAMATE-ASPARTATE SYMPORTER
1 379 InterPro IPR001991 Sodium:dicarboxylate symporter
339 386 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm.
27 49 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
239 257 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 + 1

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

Entry Method Resolution Chain Coverage Links Status
ColabFold VK055_1219
ColabFold full sequence Viewing
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 0.838
11 0.323
1 0.319
5 0.279

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 7.38 0.386
2 5.91 0.289
3 3.5 0.128
4 2.81 0.087
5 2.05 0.045

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.

86 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
6OU O59010 718.0 Da LogP 11.05 TPSA 134.4 2 viol. ✓ Clean CCCCCCCCCCCCCCCC(=O)OC[C@H](COP(=O)(O)OCCN)OC(=…
6Z6 Q15758 422.5 Da LogP 5.06 TPSA 85.3 1 viol. ✓ Clean COc1ccc(cc1)C2C(=C(OC3=C2C(=O)CC(C3)c4cccc5c4cc…
BCS O59010 211.3 Da LogP 1.33 TPSA 63.3 ✓ Ro5 ✓ Clean c1ccc(cc1)CSC[C@@H](C(=O)O)N
DAS Q5JID0 133.1 Da LogP -1.13 TPSA 100.6 ✓ Ro5 ✓ Clean C([C@H](C(=O)O)N)C(=O)O
DMU Q5JID0 482.6 Da LogP -1.23 TPSA 178.5 2 viol. ✓ Clean CCCCCCCCCCO[C@H]1[C@@H]([C@H]([C@@H]([C@H](O1)C…
PLM O59010 256.4 Da LogP 5.55 TPSA 37.3 1 viol. ✓ Clean CCCCCCCCCCCCCCCC(=O)O
QJW Q5JID0 284.2 Da LogP -0.02 TPSA 153.0 ✓ Ro5 ✓ Clean c1ccc(c(c1)CO[C@@H]([C@@H](C(=O)O)N)C(=O)O)N(=O…
QM5 Q5JID0 375.4 Da LogP 1.52 TPSA 143.1 ✓ Ro5 ✓ Clean COc1ccc(cc1)NNc2ccc(cc2)CO[C@@H]([C@@H](C(=O)O)…
TB1 Q5JID0 239.2 Da LogP 0.07 TPSA 109.9 ✓ Ro5 ✓ Clean c1ccc(cc1)CO[C@@H]([C@@H](C(=O)O)N)C(=O)O
TG2 Q15758 311.3 Da LogP 2.33 TPSA 75.6 ✓ Ro5 ✓ Clean c1ccc(cc1)c2ccc(cc2)C(=O)OC3CC(NC3)C(=O)O
TJ5 Q15758 311.3 Da LogP 2.33 TPSA 75.6 ✓ Ro5 ✓ Clean c1ccc(cc1)c2ccc(cc2)C(=O)O[C@H]3C[C@H](NC3)C(=O…
TL O59010 204.4 Da LogP -0.38 TPSA 0.0 ✓ Ro5 ✓ Clean [Tl+]

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.