Protein profile

VK055_3105

diguanylate cyclase domain protein

Genome: KpATCC43816

Gene: AIK81686.1 Structure source: AlphaFold + ColabFold UniProt A0A0H3GQ03

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Amino acids 510

Annotations 4

Features 29

PDB binders 4

Druggability 0.785

Overview

Basic information about this protein and its source genome.

Accession: VK055_3105
Assembly: Klebsiella pneumoniae subsp. pneumoniae strain ATCC 43816 KPPR1, complete genome
Gene: AIK81686.1
Status: annotated
Amino acids: 510
Structure source: AlphaFold + ColabFold

2.7.7.65

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:0052621 Catalysis of the reaction: 2 GTP = cyclic di-3',5'-guanylate + 2 diphosphate + 2 H+. GO:0005525 Binding to GTP, guanosine triphosphate.

Target profile

Computed evidence for target prioritization.

Human off-target: No hit
Human identity (%): 0.0
Gut microbiome off-target: hit
Essential (DEG): N
DEG identity (%): 35.676
Localization: CytoplasmicMembrane
ColabFold pLDDT: 90.18

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 0.785

Structure A0A0H3GQ03

Pocket Pocket 5

P2Rank 0.227

Structure A0A0H3GQ03

Pocket Pocket 1

ColabFold model

FPocket 0.709 · Pocket 12

P2Rank 0.032 · Pocket 1

Core conservation Conserved core gene

Roary core

CoreCruncher core

Gut microbiome 35 / 4744 genomes with a hit

Normalized 0.007

Sequence

Primary amino-acid sequence viewer.

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 3 GO

Enzyme Commission (EC)

2.7.7.65

Gene Ontology (GO)

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:0052621 Catalysis of the reaction: 2 GTP = cyclic di-3',5'-guanylate + 2 diphosphate + 2 H+.
GO:0005525 Binding to GTP, guanosine triphosphate.

Sequence Features

Domain/signature hits from InterPro and related databases.

29 records

Show feature table

Start	End	DB	Term	Name
382	510	ProSiteProfiles	PS50887	GGDEF domain profile.
382	510	InterPro	IPR000160	GGDEF domain
299	509	PANTHER	PTHR45138	REGULATORY COMPONENTS OF SENSORY TRANSDUCTION SYSTEM
356	506	Pfam	PF00990	Diguanylate cyclase, GGDEF domain
356	506	InterPro	IPR000160	GGDEF domain
76	272	Pfam	PF02743	Cache domain
76	272	InterPro	IPR033479	Double Cache domain 1
12	35	Phobius	TRANSMEMBRANE	Region of a membrane-bound protein predicted to be embedded in the membrane.
96	191	Gene3D	G3DSA:3.30.450.20	PAS domain
110	195	SUPERFAMILY	SSF103190	Sensory domain-like
110	195	InterPro	IPR029151	Periplasmic sensor-like domain superfamily
342	508	Gene3D	G3DSA:3.30.70.270	-
342	508	InterPro	IPR043128	Reverse transcriptase/Diguanylate cyclase domain
13	35	TMHMM	TMhelix	Region of a membrane-bound protein predicted to be embedded in the membrane.
192	278	Gene3D	G3DSA:3.30.450.20	PAS domain
64	193	CDD	cd18773	PDC1_HK_sensor
361	508	SUPERFAMILY	SSF55073	Nucleotide cyclase
361	508	InterPro	IPR029787	Nucleotide cyclase
36	288	Phobius	NON_CYTOPLASMIC_DOMAIN	Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
309	510	Phobius	CYTOPLASMIC_DOMAIN	Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm.
354	507	NCBIfam	TIGR00254	diguanylate cyclase (GGDEF) domain
354	507	InterPro	IPR000160	GGDEF domain
343	510	SMART	SM00267	duf1_3
343	510	InterPro	IPR000160	GGDEF domain
357	507	CDD	cd01949	GGDEF
357	507	InterPro	IPR000160	GGDEF domain
1	11	Phobius	CYTOPLASMIC_DOMAIN	Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm.
289	308	Phobius	TRANSMEMBRANE	Region of a membrane-bound protein predicted to be embedded in the membrane.
289	308	TMHMM	TMhelix	Region of a membrane-bound protein predicted to be embedded in the membrane.

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...

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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_A0A0H3GQ03	AlphaFold	—	—	full sequence	—	Viewing
ColabFold VK055_3105	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
5				0.785
12				0.392
1				0.363

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	Score	Probability
1	5.28	0.247
2	1.86	0.036
3	1.43	0.019

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
12				0.709
2				0.414
9				0.404

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	Score	Probability
1	1.53	0.023
2	1.37	0.016
3	1.01	0.006

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.

54 records

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.

Ligand	Source crystal	UniProt (homolog)	MW · LogP · TPSA	Lipinski	PAINS	SMILES
C2E	6TTR	A0A0H3CAN8	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…`
GAV	4H54	P31129	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…`
TAR	3TVK	P31129	150.1 Da LogP -2.12 TPSA 115.1	✓ Ro5	✓ Clean	`[C@H]([C@@H](C(=O)O)O)(C(=O)O)O`
TLA	3I5B	Q9HXT9	150.1 Da LogP -2.12 TPSA 115.1	✓ Ro5	✓ Clean	`[C@@H]([C@H](C(=O)O)O)(C(=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	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	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	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	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]…`
ZINC4095503	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	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	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	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	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…`
ZINC12359024	0.692	210.1 Da LogP -3.40 TPSA 155.5	1 viol.	✓ Clean	`O=C(O)[C@@H](O)[C@H](O)[C@H](O)[C@@H](O)C(=O)O`
ZINC13533920	0.692	210.1 Da LogP -3.40 TPSA 155.5	1 viol.	✓ Clean	`O=C(O)[C@@H](O)[C@H](O)[C@@H](O)[C@@H](O)C(=O)O`
ZINC1532740	0.692	210.1 Da LogP -3.40 TPSA 155.5	1 viol.	✓ Clean	`O=C(O)[C@@H](O)[C@H](O)[C@@H](O)[C@H](O)C(=O)O`
ZINC1549593	0.692	210.1 Da LogP -3.40 TPSA 155.5	1 viol.	✓ Clean	`O=C(O)[C@H](O)[C@H](O)[C@@H](O)[C@@H](O)C(=O)O`
ZINC2013424	0.692	210.1 Da LogP -3.40 TPSA 155.5	1 viol.	✓ Clean	`O=C(O)[C@@H](O)[C@@H](O)[C@@H](O)[C@H](O)C(=O)O`
ZINC3581021	0.692	210.1 Da LogP -3.40 TPSA 155.5	1 viol.	✓ Clean	`O=C(O)[C@H](O)[C@@H](O)[C@@H](O)[C@@H](O)C(=O)O`
ZINC3860635	0.692	210.1 Da LogP -3.40 TPSA 155.5	1 viol.	✓ Clean	`O=C(O)[C@@H](O)[C@@H](O)[C@H](O)[C@H](O)C(=O)O`
ZINC5783661	0.692	210.1 Da LogP -3.40 TPSA 155.5	1 viol.	✓ Clean	`O=C(O)[C@@H](O)[C@@H](O)[C@H](O)[C@@H](O)C(=O)O`
ZINC6072527	0.692	210.1 Da LogP -3.40 TPSA 155.5	1 viol.	✓ Clean	`O=C(O)[C@@H](O)[C@@H](O)[C@@H](O)[C@@H](O)C(=O)O`
ZINC25757995	0.689	346.2 Da LogP -1.81 TPSA 168.8	✓ Ro5	✓ Clean	`O=c1[nH]c(=O)c2ncn([C@H]3O[C@H]4CO[P@](=O)(O)O[…`
ZINC25757999	0.689	346.2 Da LogP -1.81 TPSA 168.8	✓ Ro5	✓ Clean	`O=c1[nH]c(=O)c2ncn([C@H]3O[C@H]4CO[P@@](=O)(O)O…`
ZINC4095873	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…`
ZINC2390993	0.683	424.1 Da LogP -0.76 TPSA 174.8	✓ Ro5	✓ Clean	`Nc1nc2c(nc(Br)n2[C@H]2O[C@@H]3CO[P@@](=O)(O)O[C…`
ZINC34046802	0.683	424.1 Da LogP -0.76 TPSA 174.8	✓ Ro5	✓ Clean	`Nc1nc2c(nc(Br)n2[C@@H]2O[C@H]3CO[P@@](=O)(O)O[C…`
ZINC3871269	0.683	424.1 Da LogP -0.76 TPSA 174.8	✓ Ro5	✓ Clean	`Nc1nc2c(nc(Br)n2[C@@H]2O[C@@H]3CO[P@@](=O)(O)O[…`
ZINC3871271	0.683	424.1 Da LogP -0.76 TPSA 174.8	✓ Ro5	✓ Clean	`Nc1nc2c(nc(Br)n2[C@@H]2O[C@@H]3CO[P@@](=O)(O)O[…`
ZINC4475080	0.683	424.1 Da LogP -0.76 TPSA 174.8	✓ Ro5	✓ Clean	`Nc1nc2c(nc(Br)n2[C@@H]2O[C@@H]3CO[P@@](=O)(O)O[…`
ZINC4654944	0.683	424.1 Da LogP -0.76 TPSA 174.8	✓ Ro5	✓ Clean	`Nc1nc2c(nc(Br)n2[C@@H]2O[C@@H]3CO[P@@](=O)(O)O[…`
ZINC12502230	0.672	329.2 Da LogP -0.82 TPSA 154.8	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@@H]2CO[P@](=O)(O)O[C@@…`
ZINC3581269	0.672	329.2 Da LogP -0.82 TPSA 154.8	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@@H]2CO[P@](=O)(O)O[C@H…`
ZINC3869448	0.672	329.2 Da LogP -0.82 TPSA 154.8	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@H]1O[C@H]2CO[P@](=O)(O)O[C@@H]…`
ZINC3869449	0.672	329.2 Da LogP -0.82 TPSA 154.8	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@H]2CO[P@](=O)(O)O[C@@H…`
ZINC3869450	0.672	329.2 Da LogP -0.82 TPSA 154.8	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@H]1O[C@H]2CO[P@](=O)(O)O[C@@H]…`
ZINC3869451	0.672	329.2 Da LogP -0.82 TPSA 154.8	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@H]2CO[P@](=O)(O)O[C@@H…`
ZINC3873977	0.672	329.2 Da LogP -0.82 TPSA 154.8	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@@H]2CO[P@](=O)(O)O[C@H…`
ZINC4245698	0.672	329.2 Da LogP -0.82 TPSA 154.8	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@@H]2CO[P@](=O)(O)O[C@@…`
ZINC28966567	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	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	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	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	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	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@…`
ZINC1530371	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	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	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	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	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	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	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	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	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)(…`

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.