Protein profile
VK055_0034
CDP-diacylglycerol--glycerol-3-phosphate 3-phosphatidyltransferase
Genome: KpATCC43816
Overview
Basic information about this protein and its source genome.
- Accession
- VK055_0034
- Gene
- AIK78665.1 pgsA
- Status
- annotated
- Amino acids
- 182
- Structure source
- AlphaFold + ColabFold
Target profile
Computed evidence for target prioritization.
- Human off-target
- hit
- Human identity (%)
- 41.333
- Human E-value
- 1.83e-08
- Gut microbiome off-target
- hit
- Essential (DEG)
- Y
- DEG identity (%)
- 90.11
- DEG E-value
- 2.5800000000000003e-116
- Localization
- CytoplasmicMembrane
- ColabFold pLDDT
- 89.99
Selected Druggability evidence
AlphaFold / UniProt modelSelected 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.
Sequence
Primary amino-acid sequence viewer.
Functional Annotations
Enzyme classification and Gene Ontology terms linked to this protein.
Enzyme Commission (EC)
1Gene Ontology (GO)
6- GO:0016020 A lipid bilayer along with all the proteins and protein complexes embedded in it and attached to it.
- GO:0008654 The chemical reactions and pathways resulting in the formation of a phospholipid, a lipid containing phosphoric acid as a mono- or diester.
- GO:0008444 Catalysis of the reaction: sn-glycerol 3-phosphate + CDP-diacylglycerol = 3-(3-sn-phosphatidyl)-sn-glycerol 1-phosphate + CMP + H+.
- GO:0016780 Catalysis of the transfer of a substituted phosphate group, other than diphosphate or nucleotidyl residues, from one compound (donor) to a another (acceptor).
- 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:0006655 The chemical reactions and pathways resulting in the formation of phosphatidylglycerols, any of a class of phospholipids in which the phosphatidyl group is esterified to the hydroxyl group of glycerol.
Sequence Features
Domain/signature hits from InterPro and related databases.
Show feature table
| Start | End | DB | Term | Name |
|---|---|---|---|---|
| 3 | 157 | PANTHER | PTHR14269 | CDP-DIACYLGLYCEROL--GLYCEROL-3-PHOSPHATE 3-PHOSPHATIDYLTRANSFERASE-RELATED |
| 7 | 26 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. |
| 149 | 169 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. |
| 84 | 88 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. |
| 64 | 83 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. |
| 7 | 25 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. |
| 170 | 182 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. |
| 53 | 63 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. |
| 109 | 119 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. |
| 26 | 30 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. |
| 120 | 143 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. |
| 49 | 71 | ProSitePatterns | PS00379 | CDP-alcohol phosphatidyltransferases signature. |
| 49 | 71 | InterPro | IPR000462 | CDP-alcohol phosphatidyltransferase |
| 3 | 165 | Pfam | PF01066 | CDP-alcohol phosphatidyltransferase |
| 3 | 165 | InterPro | IPR000462 | CDP-alcohol phosphatidyltransferase |
| 3 | 179 | FunFam | G3DSA:1.20.120.1760:FF:000001 | CDP-diacylglycerol--glycerol-3-phosphate 3-phosphatidyltransferase |
| 1 | 177 | PIRSF | PIRSF000847 | Phos_ph_gly_syn |
| 1 | 177 | InterPro | IPR004570 | CDP-diacylglycerol--glycerol-3-phosphate 3-phosphatidyltransferase |
| 144 | 148 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. |
| 121 | 143 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. |
| 1 | 182 | Hamap | MF_01437 | CDP-diacylglycerol--glycerol-3-phosphate 3-phosphatidyltransferase [pgsA]. |
| 1 | 182 | InterPro | IPR023762 | CDP-diacylglycerol--glycerol-3-phosphate 3-phosphatidyltransferase, bacterial |
| 3 | 180 | NCBIfam | TIGR00560 | CDP-diacylglycerol--glycerol-3-phosphate 3-phosphatidyltransferase |
| 3 | 180 | InterPro | IPR004570 | CDP-diacylglycerol--glycerol-3-phosphate 3-phosphatidyltransferase |
| 31 | 52 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. |
| 89 | 108 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. |
| 30 | 52 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. |
| 147 | 169 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. |
| 1 | 6 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. |
| 3 | 178 | Gene3D | G3DSA:1.20.120.1760 | - |
| 3 | 178 | InterPro | IPR043130 | CDP-alcohol phosphatidyltransferase, transmembrane domain |
3D Structure
Selected loaded structure. Experimental PDB entries may cover only a portion of the sequence; predicted models typically cover the full protein.
Loading 3D structure...
Structural evidence
0 + 2Experimental PDB entries and predicted models. Click Switch to display a different structure in the viewer.
| Entry | Method | Resolution | Chain | Coverage | Links | Status |
|---|---|---|---|---|---|---|
|
AlphaFold
AF_A0A377ZDH9
|
AlphaFold | — | — | full sequence | — | Viewing |
|
ColabFold
VK055_0034
|
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 |
|---|---|---|---|---|---|---|---|
| 1 | 0.599 |
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 | 2.77 | 0.085 | ||||||
| 2 | 2.7 | 0.081 | ||||||
| 3 | 1.58 | 0.024 | ||||||
| 4 | 1.29 | 0.014 |
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 |
|---|---|---|---|---|---|---|---|
| 9 | 0.729 | ||||||
| 3 | 0.562 | ||||||
| 5 | 0.251 | ||||||
| 15 | 0.202 |
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 | 3.08 | 0.103 | ||||||
| 2 | 2.68 | 0.079 | ||||||
| 3 | 1.57 | 0.024 | ||||||
| 4 | 1.36 | 0.016 |
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.
Highest-confidence structural evidence: ligands co-crystallized with this exact protein. If the source PDB is loaded in TPW, use Open crystal to inspect it in the structure viewer.
No PDB structure with a co-crystallized ligand found for this exact protein.
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.
No PDB ligands found through similar proteins.
Experimental bioactivity from ChEMBL measured directly on this protein. Score = pchembl (−log Ki/IC₅₀; higher = more potent).
No ChEMBL bioactivity data found for this exact protein.
Bioactivity inferred from similar proteins in ChEMBL. Score = pchembl (−log Ki/IC₅₀; higher = more potent).
| Ligand | UniProt (homolog) | pchembl | MW · LogP · TPSA | Lipinski | PAINS | SMILES |
|---|---|---|---|---|---|---|
| DXH | O14735 | 9.00 | 503.5 Da LogP 5.75 TPSA 97.6 | 2 viol. | ✓ Clean |
Cc1ccc(cc1Nc2c3cnn(c3nc(n2)c4cccnc4)C)C(=O)Nc5c…
|
| DWT | O14735 | 7.24 | 503.5 Da LogP 5.75 TPSA 97.6 | 2 viol. | ✓ Clean |
Cc1ccc(cc1Nc2c3cn(nc3nc(n2)c4cccnc4)C)C(=O)Nc5c…
|
| FCN | P0ABF8 | — | 138.1 Da LogP -0.09 TPSA 70.1 | ✓ Ro5 | ✓ Clean |
C[C@H]1[C@H](O1)P(=O)(O)O
|
Proposed virtual-screening candidates from ZINC. Score = Tanimoto similarity to a known binder (0–1; higher = more similar).
| Ligand | Tanimoto | MW · LogP · TPSA | Lipinski | PAINS | SMILES |
|---|---|---|---|---|---|
| ZINC220133900 | 0.538 | 398.3 Da LogP 3.77 TPSA 85.1 | ✓ Ro5 | ✓ Clean |
Cc1nc2nc(-c3cccnc3)nn2cc1C(=O)Nc1cccc(C(F)(F)F)…
|
| ZINC20148987 | 0.532 | 414.4 Da LogP 4.50 TPSA 97.1 | ✓ Ro5 | ✓ Clean |
Cc1ccc(C(=O)Nc2cccc(C(F)(F)F)c2)cc1Nc1cncc(C(N)…
|
| ZINC9306398 | 0.512 | 398.3 Da LogP 3.77 TPSA 85.1 | ✓ Ro5 | ✓ Clean |
Cc1c(C(=O)Nc2cccc(C(F)(F)F)c2)cnc2nc(-c3cccnc3)…
|
| ZINC5049572 | 0.507 | 336.3 Da LogP 4.22 TPSA 58.2 | ✓ Ro5 | ✓ Clean |
CC(=O)Nc1cc(C(=O)Nc2cccc(C(F)(F)F)c2)ccc1C
|
| ZINC72174470 | 0.507 | 360.4 Da LogP 2.73 TPSA 93.4 | ✓ Ro5 | ✓ Clean |
Cn1ncc2c(NCCCNc3cccnc3)nc(-c3cccnc3)nc21
|
| ZINC72149792 | 0.506 | 360.4 Da LogP 2.65 TPSA 93.4 | ✓ Ro5 | ✓ Clean |
Cc1cnccc1NCCNc1nc(-c2cccnc2)nc2c1cnn2C
|
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.