Protein profile

VK055_4575

diguanylate cyclase domain protein

Genome: KpATCC43816

Gene: AIK83113.1 Structure source: AlphaFold + ColabFold UniProt A0A0H3GTW8

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Amino acids 379

Annotations 2

Features 30

PDB binders 4

Druggability 0.986

Overview

Basic information about this protein and its source genome.

Accession: VK055_4575
Assembly: Klebsiella pneumoniae subsp. pneumoniae strain ATCC 43816 KPPR1, complete genome
Gene: AIK83113.1
Status: annotated
Amino acids: 379
Structure source: AlphaFold + ColabFold

GO:0016020 A lipid bilayer along with all the proteins and protein complexes embedded in it and attached to it. GO:0007165 The cellular process in which a signal is conveyed to trigger a change in the activity or state of a cell. Signal transduction begins with reception of a signal (e.g. a ligand binding to a receptor or receptor activation by a stimulus such as light), or for signal transduction in the absence of ligand, signal-withdrawal or the activity of a constitutively active receptor. Signal transduction ends with regulation of a downstream cellular process, e.g. regulation of transcription or regulation of a metabolic process. Signal transduction covers signaling from receptors located on the surface of the cell and signaling via molecules located within the cell. For signaling between cells, signal transduction is restricted to events at and within the receiving cell.

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 (%): 36.879
Localization: CytoplasmicMembrane
ColabFold pLDDT: 88.53

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 0.986

Structure A0A0H3GTW8

Pocket Pocket 1

P2Rank 0.105

Structure A0A0H3GTW8

Pocket Pocket 1

ColabFold model

FPocket 0.882 · Pocket 2

P2Rank 0.108 · Pocket 1

Core conservation Conserved core gene

Roary core

CoreCruncher core

Gut microbiome 51 / 4744 genomes with a hit

Normalized 0.011

Sequence

Primary amino-acid sequence viewer.

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

2 GO

Gene Ontology (GO)

GO:0016020 A lipid bilayer along with all the proteins and protein complexes embedded in it and attached to it.
GO:0007165 The cellular process in which a signal is conveyed to trigger a change in the activity or state of a cell. Signal transduction begins with reception of a signal (e.g. a ligand binding to a receptor or receptor activation by a stimulus such as light), or for signal transduction in the absence of ligand, signal-withdrawal or the activity of a constitutively active receptor. Signal transduction ends with regulation of a downstream cellular process, e.g. regulation of transcription or regulation of a metabolic process. Signal transduction covers signaling from receptors located on the surface of the cell and signaling via molecules located within the cell. For signaling between cells, signal transduction is restricted to events at and within the receiving cell.

Sequence Features

Domain/signature hits from InterPro and related databases.

30 records

Show feature table

Start	End	DB	Term	Name
221	373	CDD	cd01949	GGDEF
221	373	InterPro	IPR000160	GGDEF domain
1	20	Phobius	SIGNAL_PEPTIDE	Signal peptide region
154	207	ProSiteProfiles	PS50885	HAMP domain profile.
154	207	InterPro	IPR003660	HAMP domain
122	148	Phobius	TRANSMEMBRANE	Region of a membrane-bound protein predicted to be embedded in the membrane.
3	16	Phobius	SIGNAL_PEPTIDE_H_REGION	Hydrophobic region of a signal peptide.
221	373	Pfam	PF00990	Diguanylate cyclase, GGDEF domain
17	20	Phobius	SIGNAL_PEPTIDE_C_REGION	C-terminal region of a signal peptide.
1	2	Phobius	SIGNAL_PEPTIDE_N_REGION	N-terminal region of a signal peptide.
16	116	Pfam	PF17152	Periplasmic sensor domain
16	116	InterPro	IPR033417	Periplasmic sensor domain CHASE8
117	208	Gene3D	G3DSA:6.10.340.10	-
193	372	PANTHER	PTHR46663	DIGUANYLATE CYCLASE DGCT-RELATED
126	148	TMHMM	TMhelix	Region of a membrane-bound protein predicted to be embedded in the membrane.
209	377	SMART	SM00267	duf1_3
209	377	InterPro	IPR000160	GGDEF domain
218	373	NCBIfam	TIGR00254	diguanylate cyclase (GGDEF) domain
218	373	InterPro	IPR000160	GGDEF domain
21	121	Phobius	NON_CYTOPLASMIC_DOMAIN	Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
149	379	Phobius	CYTOPLASMIC_DOMAIN	Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm.
195	215	Coils	Coil	Coil
209	377	Gene3D	G3DSA:3.30.70.270	-
209	377	InterPro	IPR043128	Reverse transcriptase/Diguanylate cyclase domain
209	378	FunFam	G3DSA:3.30.70.270:FF:000017	Predicted diguanylate cyclase
1	20	SignalP_EUK	SignalP-noTM	SignalP-noTM
225	373	SUPERFAMILY	SSF55073	Nucleotide cyclase
225	373	InterPro	IPR029787	Nucleotide cyclase
249	379	ProSiteProfiles	PS50887	GGDEF domain profile.
249	379	InterPro	IPR000160	GGDEF 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...

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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_A0A0H3GTW8	AlphaFold	—	—	full sequence	—	Viewing
ColabFold VK055_4575	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				0.986

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	1.83	0.035
2	1.67	0.028
3	1.35	0.016

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				0.882

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	1.68	0.029
2	1.55	0.023
3	1.26	0.012

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
BEZ	4ZVC	P0AA89	122.1 Da LogP 1.38 TPSA 37.3	✓ Ro5	✓ Clean	`c1ccc(cc1)C(=O)O`
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	4ZVF	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…`
TBU	4IOB	Q9I4L5	74.1 Da LogP 0.78 TPSA 20.2	✓ Ro5	✓ Clean	`CC(C)(C)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]…`
ZINC3269660	0.824	254.2 Da LogP 2.45 TPSA 71.4	✓ Ro5	Alert	`O=C(O)c1ccc(C(=O)C(=O)c2ccccc2)cc1`
ZINC2504355	0.778	226.2 Da LogP 2.62 TPSA 54.4	✓ Ro5	✓ Clean	`O=C(O)c1ccc(C(=O)c2ccccc2)cc1`
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@…`
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…`
ZINC1672966	0.688	210.2 Da LogP 2.75 TPSA 34.1	✓ Ro5	Alert	`O=C(C(=O)c1ccccc1)c1ccccc1`
ZINC34057267	0.684	274.3 Da LogP 4.72 TPSA 37.3	✓ Ro5	✓ Clean	`O=C(O)c1ccc(-c2ccc(-c3ccccc3)cc2)cc1`
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@…`
ZINC114185151	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	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	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	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)(…`
ZINC38580933	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[…`
ZINC17142115	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	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	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	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	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]…`

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.