Protein target profile
VK055_5071
diguanylate cyclase domain protein
Strong target candidate with converging metabolic, structural and chemical evidence.
Automated synthesis of the evidence currently loaded. Review the underlying records before prioritizing this protein.
Main supporting evidence
Evidence coverage
Terms and data sources used on this page
PDB: experimentally determined structures from the Protein Data Bank. These are the strongest structural evidence, but may cover only part of the protein.
AlphaFold DB model: a precomputed predicted structure downloaded from AlphaFold Database/UniProt, not an experiment performed here.
ColabFold model: a predicted structure generated for this workspace; interpret it with coverage and confidence.
pLDDT: confidence score for predicted structures. High values support local geometry; low values mean the region should not drive pocket interpretation.
FPocket / P2Rank: software tools that predict possible ligand-binding pockets on a 3D structure. They are useful screening signals, not experimental validation.
Druggability: a pocket-based estimate of whether a small molecule could bind productively. It does not mean a drug already exists.
PDB ligand: a compound observed in an experimental structure. Direct same-protein records are stronger than homolog-transferred records.
ChEMBL: a public database of measured compound bioactivity. Direct entries are stronger than entries transferred from similar proteins.
ZINC: a purchasable-compound database. Here it marks proposed candidates from chemical similarity, not measured binders.
LigQ / LigQ_2: an internal Target pipeline step that gathers PDB, ChEMBL, and ZINC ligand evidence for each protein.
Off-target: sequence similarity to proteins we prefer not to hit, such as human proteins or beneficial gut microbiome proteins.
DEG: Database of Essential Genes. A match suggests the protein resembles genes known to be essential in other organisms.
Roary / CoreCruncher: pan-genome tools used to decide whether a gene is core across analyzed strains or accessory/strain-specific.
EC / GO: functional annotations: EC describes enzyme reactions; GO describes biological process, molecular function, or cellular component.
KEGG pathway: a curated metabolic route label used here to group reactions imported from the metabolic model.
Chokepoint: a metabolic reaction that is the only producer or consumer of a metabolite in the imported model.
Prioritization evidence
Selectivity, essentiality, structural confidence, conservation, and predicted binding-site evidence.
Off-target risk
- Human off-target
- No hit
- Gut microbiome similarity
- 0.7% of screened genomes Lower prevalence suggests narrower overlap with the screened gut microbiome.
Essentiality
- Essential (DEG)
- N
- DEG identity (%)
- 37.143 Higher values support similarity to known essential genes.
Localization
- Localization
- CytoplasmicMembrane
Structure confidence
- ColabFold pLDDT
- 93.75 0-100 confidence; >70 supports local structural interpretation.
Binding-site evidence
AlphaFold DB / UniProt modelThe selected pocket score is the FPocket value used for ranking after applying the curated structure priority. It estimates small-molecule pocket quality; it is not experimental binding evidence. The 3D viewer may show a different loaded structure, so visible pockets can differ.
Cross-references
External database identifiers for this protein, its structures, ligands, and metabolic reactions.
Sequence
Pathways
Sequence
Primary amino-acid sequence viewer.
MKLAGLHPDEQRRLQSLRSSGLLNSGKEERFDRLTRLARSLYNLPVASISLVGEDLLHIKSCAGLDVDTVPRDISFCAHTILQTDPLIVNDMQQDERFHDNPLVIEAPFIRFYAGYPVQLPDGATVGSFCLMDHQPRSFSAHEMQILSDLAAIVEDEFKVLDAATSDELTGLFNRRGFLTLAEYALLTAQRRHEPVSLAFVDLDRFKHINDTWGHEEGDRALIAIADLMKAAFRESDILARQGGDEFIILFANTSRHDAAAAMETLSHNVARFNQQAAHPWQLAFSWGCVEYDPAHHPSLNALVATADRLMYQAKQKQGRERR
Functional annotations
Enzyme classification and Gene Ontology terms linked to this protein.
Enzyme Commission (EC)
1Gene Ontology (GO)
2- GO:0005515 Binding to a protein.
- GO:0052621 Catalysis of the reaction: 2 GTP = cyclic di-3',5'-guanylate + 2 diphosphate + 2 H+.
Sequence domains and features
Domain and signature matches imported from InterPro and related databases.
Show feature table
| Start | End | DB | Term | Name |
|---|---|---|---|---|
| 163 | 321 | NCBIfam | TIGR00254 | diguanylate cyclase (GGDEF) domain |
| 163 | 321 | InterPro | IPR000160 | GGDEF domain |
| 10 | 153 | Gene3D | G3DSA:3.30.450.40 | - |
| 10 | 153 | InterPro | IPR029016 | GAF-like domain superfamily |
| 194 | 323 | ProSiteProfiles | PS50887 | GGDEF domain profile. |
| 194 | 323 | InterPro | IPR000160 | GGDEF domain |
| 154 | 322 | Gene3D | G3DSA:3.30.70.270 | - |
| 154 | 322 | InterPro | IPR043128 | Reverse transcriptase/Diguanylate cyclase domain |
| 154 | 322 | SMART | SM00267 | duf1_3 |
| 154 | 322 | InterPro | IPR000160 | GGDEF domain |
| 159 | 323 | FunFam | G3DSA:3.30.70.270:FF:000001 | Diguanylate cyclase domain protein |
| 26 | 168 | SMART | SM00065 | gaf_1 |
| 26 | 168 | InterPro | IPR003018 | GAF domain |
| 28 | 155 | Pfam | PF01590 | GAF domain |
| 28 | 155 | InterPro | IPR003018 | GAF domain |
| 167 | 322 | CDD | cd01949 | GGDEF |
| 167 | 322 | InterPro | IPR000160 | GGDEF domain |
| 164 | 318 | Pfam | PF00990 | Diguanylate cyclase, GGDEF domain |
| 164 | 318 | InterPro | IPR000160 | GGDEF domain |
| 28 | 154 | SUPERFAMILY | SSF55781 | GAF domain-like |
| 169 | 318 | SUPERFAMILY | SSF55073 | Nucleotide cyclase |
| 169 | 318 | InterPro | IPR029787 | Nucleotide cyclase |
| 16 | 322 | PANTHER | PTHR45138 | REGULATORY COMPONENTS OF SENSORY TRANSDUCTION SYSTEM |
3D structure
Selected loaded structure. Experimental PDB entries may cover only a portion of the sequence; AlphaFold DB and ColabFold models typically cover the full protein but remain computational predictions.
How colors and pocket overlays are used
Pocket details Inspect a specific pocket, or open the full viewer
- Method
- -
- Score
- -
- Visible layer
- -
- Residues
- -
- Pocket properties
- -
Selecting a pocket opens its details and centers the viewer without clearing other active layers. Use Focus this pocket when you want to hide the rest; use Surface for the wider residue environment.
Binding pockets · FPocket
Druggability: high ≥ 0.7 · medium 0.4–0.69 · low < 0.4
Binding pockets · P2Rank
Probability: high ≥ 0.5 · medium 0.2–0.49 · low < 0.2
Binding pockets · FPocket
Druggability: high ≥ 0.7 · medium 0.4–0.69 · low < 0.4
Binding pockets · P2Rank
Probability: high ≥ 0.5 · medium 0.2–0.49 · low < 0.2
All structural evidence
Structural evidence
0 + 2Experimental PDB entries plus predicted AlphaFold DB or ColabFold models. Click Switch to display a different loaded structure in the viewer.
| Entry | Method | Resolution | Chain | Coverage | Links | Status |
|---|---|---|---|---|---|---|
|
AlphaFold DB
AF_A0A0H3GVP9
|
AlphaFold DB | — | — | full sequence | — | Viewing |
|
ColabFold
VK055_5071
|
ColabFold | — | — | full sequence | — | Loaded |
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.
Structural ligand evidence is available for this target.
Highest-confidence structural evidence: ligands co-crystallized with this exact protein. If the source PDB is loaded in Target, 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.
| Ligand | Source crystal | UniProt (homolog) | MW · LogP · TPSA | Lipinski | PAINS | SMILES |
|---|---|---|---|---|---|---|
| BEZ RCSB PDB | P0AA89 | 122.1 Da LogP 1.38 TPSA 37.3 | ✓ Ro5 | ✓ Clean |
c1ccc(cc1)C(=O)O
|
|
| C2E RCSB PDB | Q886S7 | 690.4 Da LogP -3.05 TPSA 349.6 | 3 viol. | ✓ Clean |
c1nc2c(n1[C@H]3[C@@H]([C@H]4[C@H](O3)CO[P@@](=O…
|
|
| CYC RCSB PDB | Q55434 | 588.7 Da LogP 5.19 TPSA 160.9 | 2 viol. | ✓ Clean |
CC[C@@H]\1[C@H](C(=O)N/C1=C\c2c(c(c([nH]2)/C=C\…
|
|
| GAV RCSB PDB | P0AA89 | 539.2 Da LogP -1.40 TPSA 278.9 | 3 viol. | ✓ Clean |
c1nc2c(n1[C@H]3[C@@H]([C@@H]([C@H](O3)CO[P@](=O…
|
|
| POP RCSB PDB | Q39UD1 | 176.0 Da LogP -2.08 TPSA 129.9 | ✓ Ro5 | ✓ Clean |
O[P@@](=O)([O-])O[P@@](=O)(O)[O-]
|
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).
No ChEMBL hits found through similar proteins.
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 |
|---|---|---|---|---|---|
| ZINC12501894 ZINC | 1.000 | 345.2 Da LogP -1.52 TPSA 174.8 | ✓ Ro5 | ✓ Clean |
Nc1nc2c(ncn2[C@@H]2O[C@@H]3CO[P@](=O)(O)O[C@@H]…
|
| ZINC33494013 ZINC | 1.000 | 345.2 Da LogP -1.52 TPSA 174.8 | ✓ Ro5 | ✓ Clean |
Nc1nc2c(ncn2[C@@H]2O[C@@H]3CO[P@](=O)(O)O[C@@H]…
|
| ZINC4095501 ZINC | 1.000 | 345.2 Da LogP -1.52 TPSA 174.8 | ✓ Ro5 | ✓ Clean |
Nc1nc2c(ncn2[C@@H]2O[C@@H]3CO[P@](=O)(O)O[C@H]3…
|
| ZINC88465990 ZINC | 1.000 | 345.2 Da LogP -1.52 TPSA 174.8 | ✓ Ro5 | ✓ Clean |
Nc1nc2c(ncn2[C@@H]2O[C@@H]3CO[P@@](=O)(O)O[C@H]…
|
| ZINC35000839 ZINC | 0.867 | 443.2 Da LogP -2.45 TPSA 252.6 | 2 viol. | ✓ Clean |
Nc1nc2c(ncn2[C@H]2O[C@@H](CO[P@@](=O)(O)OP(=O)(…
|
| ZINC3269660 ZINC | 0.824 | 254.2 Da LogP 2.45 TPSA 71.4 | ✓ Ro5 | Alert |
O=C(O)c1ccc(C(=O)C(=O)c2ccccc2)cc1
|
| ZINC2504355 ZINC | 0.778 | 226.2 Da LogP 2.62 TPSA 54.4 | ✓ Ro5 | ✓ Clean |
O=C(O)c1ccc(C(=O)c2ccccc2)cc1
|
| ZINC4095503 ZINC | 0.746 | 330.2 Da LogP -1.11 TPSA 148.8 | ✓ Ro5 | ✓ Clean |
O=c1[nH]cnc2c1ncn2[C@@H]1O[C@@H]2CO[P@](=O)(O)O…
|
| ZINC4533542 ZINC | 0.746 | 330.2 Da LogP -1.11 TPSA 148.8 | ✓ Ro5 | ✓ Clean |
O=c1[nH]cnc2c1ncn2[C@H]1O[C@H]2CO[P@](=O)(O)O[C…
|
| ZINC4533545 ZINC | 0.746 | 330.2 Da LogP -1.11 TPSA 148.8 | ✓ Ro5 | ✓ Clean |
O=c1[nH]cnc2c1ncn2[C@H]1O[C@H]2CO[P@](=O)(O)O[C…
|
| ZINC28711394 ZINC | 0.706 | 415.3 Da LogP -0.17 TPSA 180.9 | 1 viol. | ✓ Clean |
CCCC(=O)O[C@@H]1[C@@H]2O[P@](=O)(O)OC[C@H]2O[C@…
|
| ZINC13515981 ZINC | 0.701 | 415.3 Da LogP -0.37 TPSA 177.9 | ✓ Ro5 | ✓ Clean |
CCCC(=O)Nc1nc2c(ncn2[C@@H]2O[C@@H]3CO[P@](=O)(O…
|
| ZINC4095873 ZINC | 0.689 | 329.2 Da LogP -0.49 TPSA 154.6 | ✓ Ro5 | ✓ Clean |
Nc1nc2c(ncn2[C@H]2C[C@@H]3O[P@@](=O)(O)OC[C@H]3…
|
| ZINC1672966 ZINC | 0.688 | 210.2 Da LogP 2.75 TPSA 34.1 | ✓ Ro5 | Alert |
O=C(C(=O)c1ccccc1)c1ccccc1
|
| ZINC34057267 ZINC | 0.684 | 274.3 Da LogP 4.72 TPSA 37.3 | ✓ Ro5 | ✓ Clean |
O=C(O)c1ccc(-c2ccc(-c3ccccc3)cc2)cc1
|
| ZINC28966567 ZINC | 0.671 | 478.4 Da LogP 0.38 TPSA 192.9 | 1 viol. | ✓ Clean |
CNc1ccccc1C(=O)O[C@@H]1[C@@H]2O[P@](=O)(O)OC[C@…
|
| ZINC5080458 ZINC | 0.656 | 323.3 Da LogP -0.89 TPSA 137.5 | ✓ Ro5 | ✓ Clean |
CC1(C)OC[C@H]2O[C@@H](n3cnc4c(=O)[nH]c(N)nc43)[…
|
| ZINC5080460 ZINC | 0.656 | 323.3 Da LogP -0.89 TPSA 137.5 | ✓ Ro5 | ✓ Clean |
CC1(C)OC[C@@H]2O[C@@H](n3cnc4c(=O)[nH]c(N)nc43)…
|
| ZINC5080462 ZINC | 0.656 | 323.3 Da LogP -0.89 TPSA 137.5 | ✓ Ro5 | ✓ Clean |
CC1(C)OC[C@H]2O[C@@H](n3cnc4c(=O)[nH]c(N)nc43)[…
|
| ZINC5080463 ZINC | 0.656 | 323.3 Da LogP -0.89 TPSA 137.5 | ✓ Ro5 | ✓ Clean |
CC1(C)OC[C@@H]2O[C@@H](n3cnc4c(=O)[nH]c(N)nc43)…
|
| ZINC38580931 ZINC | 0.651 | 345.2 Da LogP -1.58 TPSA 168.9 | ✓ Ro5 | ✓ Clean |
Nc1c2ncn([C@@H]3O[C@@H]4CO[P@](=O)(O)O[C@H]4[C@…
|
| ZINC114185151 ZINC | 0.647 | 298.2 Da LogP 2.15 TPSA 108.7 | ✓ Ro5 | Alert |
O=C(O)c1ccc(C(=O)C(=O)c2ccc(C(=O)O)cc2)cc1
|
| ZINC1590838 ZINC | 0.647 | 342.4 Da LogP 3.82 TPSA 68.3 | ✓ Ro5 | Alert |
O=C(C(=O)c1ccc(C(=O)C(=O)c2ccccc2)cc1)c1ccccc1
|
| ZINC16133932 ZINC | 0.647 | 474.5 Da LogP 4.88 TPSA 102.4 | ✓ Ro5 | Alert |
O=C(C(=O)c1ccc(C(=O)C(=O)c2ccc(C(=O)C(=O)c3cccc…
|
| ZINC1530371 ZINC | 0.645 | 345.2 Da LogP -1.52 TPSA 174.8 | ✓ Ro5 | ✓ Clean |
Nc1nc2c(ncn2[C@H]2O[C@@H](CO)[C@H]3O[P@](=O)(O)…
|
| ZINC4097050 ZINC | 0.645 | 345.2 Da LogP -1.52 TPSA 174.8 | ✓ Ro5 | ✓ Clean |
Nc1nc2c(ncn2[C@@H]2O[C@H](CO)[C@H]3O[P@](=O)(O)…
|
| ZINC4545949 ZINC | 0.645 | 345.2 Da LogP -1.52 TPSA 174.8 | ✓ Ro5 | ✓ Clean |
Nc1nc2c(ncn2[C@H]2O[C@@H](CO)[C@H]3O[P@](=O)(O)…
|
| ZINC4545950 ZINC | 0.645 | 345.2 Da LogP -1.52 TPSA 174.8 | ✓ Ro5 | ✓ Clean |
Nc1nc2c(ncn2[C@@H]2O[C@@H](CO)[C@H]3O[P@](=O)(O…
|
| ZINC4545951 ZINC | 0.645 | 345.2 Da LogP -1.52 TPSA 174.8 | ✓ Ro5 | ✓ Clean |
Nc1nc2c(ncn2[C@@H]2O[C@@H](CO)[C@H]3O[P@](=O)(O…
|
| ZINC35793709 ZINC | 0.642 | 390.2 Da LogP -1.62 TPSA 217.9 | 1 viol. | ✓ Clean |
Nc1nc2c(nc([N+](=O)[O-])n2[C@@H]2O[C@@H]3CO[P@@…
|
| ZINC25757988 ZINC | 0.641 | 346.2 Da LogP -1.40 TPSA 169.0 | ✓ Ro5 | ✓ Clean |
O=c1nc(O)[nH]c2c1ncn2[C@H]1O[C@H]2CO[P@@](=O)(O…
|
| ZINC25757992 ZINC | 0.641 | 346.2 Da LogP -1.40 TPSA 169.0 | ✓ Ro5 | ✓ Clean |
O=c1nc(O)[nH]c2c1ncn2[C@H]1O[C@H]2CO[P@@](=O)(O…
|
| ZINC38581024 ZINC | 0.641 | 346.2 Da LogP -1.40 TPSA 169.0 | ✓ Ro5 | ✓ Clean |
O=c1nc(O)[nH]c2c1ncn2[C@@H]1O[C@@H]2CO[P@](=O)(…
|
| ZINC38580933 ZINC | 0.635 | 329.2 Da LogP -0.82 TPSA 154.8 | ✓ Ro5 | ✓ Clean |
Nc1ncc2ncn([C@@H]3O[C@@H]4CO[P@](=O)(O)O[C@H]4[…
|
| ZINC101148330 ZINC | 0.634 | 445.3 Da LogP 0.81 TPSA 153.2 | ✓ Ro5 | ✓ Clean |
O=c1c2ncn([C@@H]3O[C@@H]4CO[P@](=O)(O)O[C@H]4[C…
|
| ZINC17142115 ZINC | 0.613 | 320.2 Da LogP -1.66 TPSA 172.2 | ✓ Ro5 | ✓ Clean |
NC(=O)c1ncn([C@@H]2O[C@@H]3CO[P@](=O)(O)O[C@@H]…
|
| ZINC22047759 ZINC | 0.613 | 320.2 Da LogP -1.66 TPSA 172.2 | ✓ Ro5 | ✓ Clean |
NC(=O)c1ncn([C@@H]2O[C@@H]3CO[P@](=O)(O)O[C@H]3…
|
| ZINC255997527 ZINC | 0.613 | 320.2 Da LogP -1.66 TPSA 172.2 | ✓ Ro5 | ✓ Clean |
NC(=O)c1ncn([C@@H]2O[C@@H]3CO[P@](=O)(O)O[C@H]3…
|
| ZINC33650193 ZINC | 0.613 | 320.2 Da LogP -1.66 TPSA 172.2 | ✓ Ro5 | ✓ Clean |
NC(=O)c1ncn([C@@H]2O[C@H]3CO[P@](=O)(O)O[C@H]3[…
|
| ZINC33650194 ZINC | 0.613 | 320.2 Da LogP -1.66 TPSA 172.2 | ✓ Ro5 | ✓ Clean |
NC(=O)c1ncn([C@@H]2O[C@@H]3CO[P@](=O)(O)O[C@@H]…
|
| ZINC1070912 ZINC | 0.611 | 286.3 Da LogP 4.15 TPSA 34.1 | ✓ Ro5 | ✓ Clean |
O=C(c1ccccc1)c1ccc(C(=O)c2ccccc2)cc1
|
| ZINC134079 ZINC | 0.611 | 242.2 Da LogP 2.75 TPSA 74.6 | ✓ Ro5 | ✓ Clean |
O=C(O)c1ccc(-c2ccc(C(=O)O)cc2)cc1
|
| ZINC1640789 ZINC | 0.611 | 374.3 Da LogP 3.55 TPSA 108.7 | ✓ Ro5 | ✓ Clean |
O=C(O)c1ccc(C(=O)c2ccc(C(=O)c3ccc(C(=O)O)cc3)cc…
|
| ZINC2146859 ZINC | 0.611 | 270.2 Da LogP 2.31 TPSA 91.7 | ✓ Ro5 | ✓ Clean |
O=C(O)c1ccc(C(=O)c2ccc(C(=O)O)cc2)cc1
|
| ZINC3147211 ZINC | 0.611 | 318.3 Da LogP 4.42 TPSA 74.6 | ✓ Ro5 | ✓ Clean |
O=C(O)c1ccc(-c2ccc(-c3ccc(C(=O)O)cc3)cc2)cc1
|
| ZINC25757703 ZINC | 0.609 | 330.2 Da LogP -1.11 TPSA 148.8 | ✓ Ro5 | ✓ Clean |
O=c1nc[nH]c2c1ncn2[C@H]1O[C@H]2CO[P@](=O)(O)O[C…
|
| ZINC25757707 ZINC | 0.609 | 330.2 Da LogP -1.11 TPSA 148.8 | ✓ Ro5 | ✓ Clean |
O=c1nc[nH]c2c1ncn2[C@H]1O[C@H]2CO[P@](=O)(O)O[C…
|
| ZINC22309461 ZINC | 0.603 | 487.8 Da LogP 1.28 TPSA 174.8 | 1 viol. | ✓ Clean |
Nc1nc2c(nc(Sc3ccc(Cl)cc3)n2[C@@H]2O[C@@H]3CO[P@…
|
| ZINC22309471 ZINC | 0.603 | 487.8 Da LogP 1.28 TPSA 174.8 | 1 viol. | ✓ Clean |
Nc1nc2c(nc(Sc3ccc(Cl)cc3)n2[C@@H]2O[C@@H]3CO[P@…
|
| ZINC28711406 ZINC | 0.603 | 487.8 Da LogP 1.28 TPSA 174.8 | 1 viol. | ✓ Clean |
Nc1nc2c(nc(Sc3ccc(Cl)cc3)n2[C@@H]2O[C@@H]3CO[P@…
|
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.