Protein profile

VK055_0808

diguanylate cyclase domain protein

Genome: KpATCC43816

Gene: AIK79431.1 Structure source: AlphaFold + ColabFold UniProt A0A0H3GTD8

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Amino acids 551

Annotations 0

Features 42

PDB binders 4

Druggability 0.683

Overview

Basic information about this protein and its source genome.

Accession: VK055_0808
Assembly: Klebsiella pneumoniae subsp. pneumoniae strain ATCC 43816 KPPR1, complete genome
Gene: AIK79431.1
Status: annotated
Amino acids: 551
Structure source: AlphaFold + ColabFold

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 (%): 35.698
Localization: CytoplasmicMembrane
ColabFold pLDDT: 91.68

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 0.683

Structure A0A0H3GTD8

Pocket Pocket 13

P2Rank 0.788

Structure A0A0H3GTD8

Pocket Pocket 1

ColabFold model

FPocket 0.669 · Pocket 3

P2Rank 0.793 · Pocket 1

Core conservation Conserved core gene

Roary core

CoreCruncher core

Gut microbiome 4 / 4744 genomes with a hit

Normalized 0.001

Sequence

Primary amino-acid sequence viewer.

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

No GO or EC annotations are currently loaded for this protein.

Sequence Features

Domain/signature hits from InterPro and related databases.

42 records

Show feature table

Start	End	DB	Term	Name
304	546	SMART	SM00052	duf2_2
304	546	InterPro	IPR001633	EAL domain
310	544	CDD	cd01948	EAL
310	544	InterPro	IPR001633	EAL domain
305	551	ProSiteProfiles	PS50883	EAL domain profile.
305	551	InterPro	IPR001633	EAL domain
11	129	NCBIfam	TIGR00229	PAS domain S-box protein
11	129	InterPro	IPR000014	PAS domain
310	541	Pfam	PF00563	EAL domain
310	541	InterPro	IPR001633	EAL domain
306	550	Gene3D	G3DSA:3.20.20.450	EAL domain
306	550	InterPro	IPR035919	EAL domain superfamily
141	295	SUPERFAMILY	SSF55073	Nucleotide cyclase
141	295	InterPro	IPR029787	Nucleotide cyclase
125	294	SMART	SM00267	duf1_3
125	294	InterPro	IPR000160	GGDEF domain
7	80	ProSiteProfiles	PS50112	PAS repeat profile.
7	80	InterPro	IPR000014	PAS domain
164	296	ProSiteProfiles	PS50887	GGDEF domain profile.
164	296	InterPro	IPR000160	GGDEF domain
311	547	SUPERFAMILY	SSF141868	EAL domain-like
311	547	InterPro	IPR035919	EAL domain superfamily
20	124	SUPERFAMILY	SSF55785	PYP-like sensor domain (PAS domain)
20	124	InterPro	IPR035965	PAS domain superfamily
71	134	ProSiteProfiles	PS50113	PAC domain profile.
71	134	InterPro	IPR000700	PAS-associated, C-terminal
20	122	CDD	cd00130	PAS
20	122	InterPro	IPR000014	PAS domain
120	305	Gene3D	G3DSA:3.30.70.270	-
120	305	InterPro	IPR043128	Reverse transcriptase/Diguanylate cyclase domain
137	286	CDD	cd01949	GGDEF
137	286	InterPro	IPR000160	GGDEF domain
8	119	Gene3D	G3DSA:3.30.450.20	PAS domain
83	125	SMART	SM00086	pac_2
83	125	InterPro	IPR001610	PAC motif
136	286	Pfam	PF00990	Diguanylate cyclase, GGDEF domain
136	286	InterPro	IPR000160	GGDEF domain
22	124	Pfam	PF13426	PAS domain
22	124	InterPro	IPR000014	PAS domain
22	543	PANTHER	PTHR44757	DIGUANYLATE CYCLASE DGCP
133	287	NCBIfam	TIGR00254	diguanylate cyclase (GGDEF) domain
133	287	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_A0A0H3GTD8	AlphaFold	—	—	full sequence	—	Viewing
ColabFold VK055_0808	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
13				0.683
2				0.567
5				0.001
40				0.0

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	20.12	0.788
2	3.0	0.079
3	1.82	0.029
4	1.43	0.016
5	1.36	0.013

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
3				0.669
20				0.372
2				0.001
16				0.0

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	20.4	0.793
2	2.32	0.049
3	2.0	0.036
4	1.48	0.017
5	1.29	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
C2E	3N3T	Q3SJE6	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…`
DAO	6DGG	C9XTL5	200.3 Da LogP 3.99 TPSA 37.3	✓ Ro5	✓ Clean	`CCCCCCCCCCCC(=O)O`
GEY	6DGJ	C9XTL5	198.3 Da LogP 3.77 TPSA 37.3	✓ Ro5	✓ Clean	`CCCCCCCCC/C=C\C(=O)O`
OXY	1S66	P76129	32.0 Da LogP 0.07 TPSA 34.1	✓ Ro5	✓ Clean	`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
ZINC100022626	1.000	212.3 Da LogP 4.16 TPSA 37.3	✓ Ro5	✓ Clean	`CCCCCCCCCC/C=C\C(=O)O`
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]…`
ZINC1529498	1.000	200.3 Da LogP 3.99 TPSA 37.3	✓ Ro5	✓ Clean	`CCCCCCCCCCCC(=O)O`
ZINC1530417	1.000	228.4 Da LogP 4.77 TPSA 37.3	✓ Ro5	✓ Clean	`CCCCCCCCCCCCCC(=O)O`
ZINC1628119	1.000	214.3 Da LogP 4.38 TPSA 37.3	✓ Ro5	✓ Clean	`CCCCCCCCCCCCC(=O)O`
ZINC1693736	1.000	212.3 Da LogP 4.16 TPSA 37.3	✓ Ro5	✓ Clean	`CCCCCCCCCC/C=C/C(=O)O`
ZINC2039111479	1.000	212.3 Da LogP 4.16 TPSA 37.3	✓ Ro5	✓ Clean	`CCCCCCCCCCC=CC(=O)O`
ZINC32838980	1.000	226.4 Da LogP 4.55 TPSA 37.3	✓ Ro5	✓ Clean	`CCCCCCCCCCC/C=C/C(=O)O`
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]…`
ZINC138457918	0.850	228.3 Da LogP 3.56 TPSA 54.4	✓ Ro5	✓ Clean	`CCCCCCCC(=O)CCCCC(=O)O`
ZINC138458029	0.850	228.3 Da LogP 3.56 TPSA 54.4	✓ Ro5	✓ Clean	`CCCCCCC(=O)CCCCCC(=O)O`
ZINC144395054	0.850	242.4 Da LogP 3.95 TPSA 54.4	✓ Ro5	✓ Clean	`CCCCCC(=O)CCCCCCCC(=O)O`
ZINC14619628	0.850	270.4 Da LogP 4.73 TPSA 54.4	✓ Ro5	✓ Clean	`CCCCCC(=O)CCCCCCCCCC(=O)O`
ZINC196749828	0.850	214.3 Da LogP 3.17 TPSA 54.4	✓ Ro5	✓ Clean	`CCCCCCC(=O)CCCCC(=O)O`
ZINC2113934076	0.850	256.4 Da LogP 4.34 TPSA 54.4	✓ Ro5	✓ Clean	`CCCCCCC(=O)CCCCCCCC(=O)O`
ZINC2113934082	0.850	256.4 Da LogP 4.34 TPSA 54.4	✓ Ro5	✓ Clean	`CCCCCCCC(=O)CCCCCCC(=O)O`
ZINC2113934083	0.850	256.4 Da LogP 4.34 TPSA 54.4	✓ Ro5	✓ Clean	`CCCCCCCCCC(=O)CCCCC(=O)O`
ZINC2243670	0.850	228.3 Da LogP 3.56 TPSA 54.4	✓ Ro5	✓ Clean	`CCCCCC(=O)CCCCCCC(=O)O`
ZINC2569203	0.850	214.3 Da LogP 3.17 TPSA 54.4	✓ Ro5	✓ Clean	`CCCCCC(=O)CCCCCC(=O)O`
ZINC4798470	0.850	270.4 Da LogP 4.73 TPSA 54.4	✓ Ro5	✓ Clean	`CCCCCCC(=O)CCCCCCCCC(=O)O`
ZINC5973005	0.850	242.4 Da LogP 3.95 TPSA 54.4	✓ Ro5	✓ Clean	`CCCCCCC(=O)CCCCCCC(=O)O`
ZINC71418182	0.850	270.4 Da LogP 4.73 TPSA 54.4	✓ Ro5	✓ Clean	`CCCCCCCCCCC(=O)CCCCC(=O)O`
ZINC79244776	0.850	270.4 Da LogP 4.73 TPSA 54.4	✓ Ro5	✓ Clean	`CCCCCCCC(=O)CCCCCCCC(=O)O`
ZINC86037082	0.850	270.4 Da LogP 4.73 TPSA 54.4	✓ Ro5	✓ Clean	`CCCCCCCCCC(=O)CCCCCC(=O)O`
ZINC86037089	0.850	270.4 Da LogP 4.73 TPSA 54.4	✓ Ro5	✓ Clean	`CCCCCCCCC(=O)CCCCCCC(=O)O`
ZINC86039283	0.850	242.4 Da LogP 3.95 TPSA 54.4	✓ Ro5	✓ Clean	`CCCCCCCCC(=O)CCCCC(=O)O`
ZINC3160730	0.810	214.3 Da LogP 3.17 TPSA 54.4	✓ Ro5	✓ Clean	`CCCCCCCC(=O)CCCC(=O)O`
ZINC4582907	0.810	200.3 Da LogP 2.78 TPSA 54.4	✓ Ro5	✓ Clean	`CCCCCCC(=O)CCCC(=O)O`
ZINC4727003	0.810	312.4 Da LogP 4.69 TPSA 71.4	✓ Ro5	✓ Clean	`CCCCCCC(=O)CCC(=O)CCCCCCCC(=O)O`
ZINC86037074	0.810	270.4 Da LogP 4.73 TPSA 54.4	✓ Ro5	✓ Clean	`CCCCCCCCCCCC(=O)CCCC(=O)O`
ZINC2378801	0.800	200.3 Da LogP 2.78 TPSA 54.4	✓ Ro5	✓ Clean	`CCCCCC(=O)CCCCC(=O)O`
ZINC2113934081	0.762	270.4 Da LogP 4.73 TPSA 54.4	✓ Ro5	✓ Clean	`CCCCC(=O)CCCCCCCCCCC(=O)O`
ZINC2243668	0.762	214.3 Da LogP 3.17 TPSA 54.4	✓ Ro5	✓ Clean	`CCCCC(=O)CCCCCCC(=O)O`
ZINC2378799	0.762	200.3 Da LogP 2.78 TPSA 54.4	✓ Ro5	✓ Clean	`CCCCC(=O)CCCCCC(=O)O`
ZINC33820423	0.762	242.4 Da LogP 3.95 TPSA 54.4	✓ Ro5	✓ Clean	`CCCCC(=O)CCCCCCCCC(=O)O`
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…`
ZINC2387442	0.739	246.4 Da LogP 4.34 TPSA 37.3	✓ Ro5	✓ Clean	`CCCCCCCCSCCCCC(=O)O`
ZINC31778284	0.739	310.4 Da LogP 4.47 TPSA 71.4	✓ Ro5	✓ Clean	`CCCCCCC(=O)/C=C\C(=O)CCCCCCCC(=O)O`
ZINC5540108	0.739	310.4 Da LogP 4.47 TPSA 71.4	✓ Ro5	✓ Clean	`CCCCCCC(=O)/C=C/C(=O)CCCCCCCC(=O)O`
ZINC64633397	0.739	226.4 Da LogP 4.55 TPSA 37.3	✓ Ro5	✓ Clean	`CCCCCC/C=C\CCCCCC(=O)O`
ZINC59545317	0.727	200.3 Da LogP 2.78 TPSA 54.4	✓ Ro5	✓ Clean	`CCCCCCCC(=O)CCC(=O)O`
ZINC59545320	0.727	270.4 Da LogP 4.73 TPSA 54.4	✓ Ro5	✓ Clean	`CCCCCCCCCCCCC(=O)CCC(=O)O`
ZINC59545336	0.727	214.3 Da LogP 3.17 TPSA 54.4	✓ Ro5	✓ Clean	`CCCCCCCCC(=O)CCC(=O)O`
ZINC100246029	0.708	262.4 Da LogP 3.35 TPSA 54.4	✓ Ro5	✓ Clean	`CCCCCCCC[S@](=O)CCCCC(=O)O`
ZINC14502373	0.708	258.4 Da LogP 4.13 TPSA 57.5	✓ Ro5	✓ Clean	`CCCCCC[C@H](O)CCCCCCCC(=O)O`
ZINC8220964	0.708	316.5 Da LogP 4.27 TPSA 77.8	✓ Ro5	✓ Clean	`CCCCCCCC[C@@H](O)[C@@H](O)CCCCCCCC(=O)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.