Protein profile

VK055_0079

helix-turn-helix domain, rpiR family protein

Genome: KpATCC43816

Gene: AIK78707.1 Structure source: AlphaFold + ColabFold UniProt A0A0H3GUT9

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Amino acids 289

Annotations 5

Features 21

PDB binders 3

Druggability 0.617

Overview

Basic information about this protein and its source genome.

Accession: VK055_0079
Assembly: Klebsiella pneumoniae subsp. pneumoniae strain ATCC 43816 KPPR1, complete genome
Gene: AIK78707.1
Status: annotated
Amino acids: 289
Structure source: AlphaFold + ColabFold

GO:0097367 Binding to a carbohydrate derivative. GO:1901135 The chemical reactions and pathways involving carbohydrate derivative. GO:0003700 A transcription regulator activity that modulates transcription of gene sets via selective and non-covalent binding to a specific double-stranded genomic DNA sequence (sometimes referred to as a motif) within a cis-regulatory region. Regulatory regions include promoters (proximal and distal) and enhancers. Genes are transcriptional units, and include bacterial operons. GO:0006355 Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription. GO:0003677 Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).

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 (%): 28.139
Localization: Cytoplasmic
ColabFold pLDDT: 92.28

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 0.617

Structure A0A0H3GUT9

Pocket Pocket 1

P2Rank 0.158

Structure A0A0H3GUT9

Pocket Pocket 1

ColabFold model

FPocket 0.85 · Pocket 1

P2Rank 0.13 · Pocket 1

Core conservation Accessory gene

Roary core

CoreCruncher accessory

Gut microbiome 134 / 4744 genomes with a hit

Normalized 0.028

Sequence

Primary amino-acid sequence viewer.

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

5 GO

Gene Ontology (GO)

GO:0097367 Binding to a carbohydrate derivative.
GO:1901135 The chemical reactions and pathways involving carbohydrate derivative.
GO:0003700 A transcription regulator activity that modulates transcription of gene sets via selective and non-covalent binding to a specific double-stranded genomic DNA sequence (sometimes referred to as a motif) within a cis-regulatory region. Regulatory regions include promoters (proximal and distal) and enhancers. Genes are transcriptional units, and include bacterial operons.
GO:0006355 Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
GO:0003677 Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).

Sequence Features

Domain/signature hits from InterPro and related databases.

21 records

Show feature table

Start	End	DB	Term	Name
92	277	Gene3D	G3DSA:3.40.50.10490	-
121	260	ProSiteProfiles	PS51464	SIS domain profile.
121	260	InterPro	IPR001347	SIS domain
1	78	SUPERFAMILY	SSF46689	Homeodomain-like
1	78	InterPro	IPR009057	Homeobox-like domain superfamily
124	252	Pfam	PF01380	SIS domain
124	252	InterPro	IPR001347	SIS domain
1	277	PANTHER	PTHR30514	GLUCOKINASE
1	277	InterPro	IPR047640	HTH-type transcriptional regulator RpiR-like
1	78	Gene3D	G3DSA:1.10.10.10	-
1	78	InterPro	IPR036388	Winged helix-like DNA-binding domain superfamily
1	77	FunFam	G3DSA:1.10.10.10:FF:000060	DNA-binding transcriptional regulator HexR
1	76	Pfam	PF01418	Helix-turn-helix domain, rpiR family
1	76	InterPro	IPR000281	Helix-turn-helix protein RpiR
1	77	ProSiteProfiles	PS51071	RpiR-type HTH domain profile.
1	77	InterPro	IPR000281	Helix-turn-helix protein RpiR
116	253	CDD	cd05013	SIS_RpiR
116	253	InterPro	IPR035472	RpiR-like, SIS domain
94	277	SUPERFAMILY	SSF53697	SIS domain
94	277	InterPro	IPR046348	SIS domain superfamily
92	277	FunFam	G3DSA:3.40.50.10490:FF:000009	DNA-binding transcriptional regulator HexR

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_A0A0H3GUT9	AlphaFold	—	—	full sequence	—	Viewing
ColabFold VK055_0079	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				0.617
6				0.005
23				0.003
15				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	4.49	0.158
2	3.15	0.085
3	1.52	0.018

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				0.85
2				0.573
4				0.527
9				0.028

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	4.01	0.13
2	2.7	0.065
3	1.62	0.021

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.

53 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
4QY	7EN5	P77245	301.2 Da LogP -2.96 TPSA 165.8	1 viol.	✓ Clean	`CC(=O)N[C@@H]1[C@H]([C@@H]([C@H](O[C@H]1O)COP(=…`
J79	7EN7	P77245	373.3 Da LogP -2.46 TPSA 192.1	1 viol.	✓ Clean	`C[C@H](C(=O)O)O[C@@H]1[C@H]([C@@H](O[C@@H]([C@H…`
MXE	3IWF	A0A0H2VHQ2	76.1 Da LogP -0.37 TPSA 29.5	✓ Ro5	✓ Clean	`COCCO`

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
ZINC100350901	1.000	301.2 Da LogP -2.96 TPSA 165.8	1 viol.	✓ Clean	`CC(=O)N[C@@H]1[C@H](O)O[C@H](COP(=O)(O)O)[C@H](…`
ZINC1530414	1.000	301.2 Da LogP -2.96 TPSA 165.8	1 viol.	✓ Clean	`CC(=O)N[C@@H]1[C@@H](O)O[C@@H](COP(=O)(O)O)[C@H…`
ZINC1532625	1.000	301.2 Da LogP -2.96 TPSA 165.8	1 viol.	✓ Clean	`CC(=O)N[C@H]1[C@H](O)[C@@H](O)[C@H](COP(=O)(O)O…`
ZINC245204467	1.000	301.2 Da LogP -2.96 TPSA 165.8	1 viol.	✓ Clean	`CC(=O)N[C@H]1[C@H](O)[C@@H](O)[C@@H](COP(=O)(O)…`
ZINC245204468	1.000	301.2 Da LogP -2.96 TPSA 165.8	1 viol.	✓ Clean	`CC(=O)N[C@H]1[C@H](O)[C@H](O)[C@@H](COP(=O)(O)O…`
ZINC30725207	1.000	301.2 Da LogP -2.96 TPSA 165.8	1 viol.	✓ Clean	`CC(=O)N[C@@H]1[C@H](O)O[C@H](COP(=O)(O)O)[C@@H]…`
ZINC4096363	1.000	301.2 Da LogP -2.96 TPSA 165.8	1 viol.	✓ Clean	`CC(=O)N[C@@H]1[C@@H](O)O[C@H](COP(=O)(O)O)[C@@H…`
ZINC4097100	1.000	301.2 Da LogP -2.96 TPSA 165.8	1 viol.	✓ Clean	`CC(=O)N[C@H]1[C@@H](O)O[C@H](COP(=O)(O)O)[C@@H]…`
ZINC4097101	1.000	301.2 Da LogP -2.96 TPSA 165.8	1 viol.	✓ Clean	`CC(=O)N[C@H]1[C@H](O)O[C@H](COP(=O)(O)O)[C@@H](…`
ZINC3861769	0.708	293.3 Da LogP -2.58 TPSA 145.6	✓ Ro5	✓ Clean	`CC(=O)N[C@H]1[C@@H](O)O[C@H](CO)[C@@H](O)[C@@H]…`
ZINC4096938	0.708	293.3 Da LogP -2.58 TPSA 145.6	✓ Ro5	✓ Clean	`CC(=O)N[C@H]1[C@@H](O)O[C@H](CO)[C@@H](O)[C@@H]…`
ZINC4245657	0.708	293.3 Da LogP -2.58 TPSA 145.6	✓ Ro5	✓ Clean	`CC(=O)N[C@H]1[C@@H](O)O[C@@H](CO)[C@@H](O)[C@@H…`
ZINC44608202	0.708	293.3 Da LogP -2.58 TPSA 145.6	✓ Ro5	✓ Clean	`CC(=O)N[C@H]1[C@@H](O)O[C@H](CO)[C@H](O)[C@@H]1…`
ZINC62227779	0.708	293.3 Da LogP -2.58 TPSA 145.6	✓ Ro5	✓ Clean	`CC(=O)N[C@H]1[C@H](O[C@@H](C)C(=O)O)[C@@H](O)[C…`
ZINC71755829	0.708	293.3 Da LogP -2.58 TPSA 145.6	✓ Ro5	✓ Clean	`CC(=O)N[C@@H]1[C@@H](O)O[C@H](CO)[C@@H](O)[C@@H…`
ZINC71755842	0.708	293.3 Da LogP -2.58 TPSA 145.6	✓ Ro5	✓ Clean	`CC(=O)N[C@@H]1[C@@H](O)O[C@@H](CO)[C@@H](O)[C@@…`
ZINC79670001	0.708	293.3 Da LogP -2.58 TPSA 145.6	✓ Ro5	✓ Clean	`CC(=O)N[C@H]1[C@@H](O)O[C@@H](CO)[C@@H](O)[C@@H…`
ZINC8585107	0.708	293.3 Da LogP -2.58 TPSA 145.6	✓ Ro5	✓ Clean	`CC(=O)N[C@@H]1[C@H](O)O[C@H](CO)[C@H](O)[C@@H]1…`
ZINC8585110	0.708	293.3 Da LogP -2.58 TPSA 145.6	✓ Ro5	✓ Clean	`CC(=O)N[C@@H]1[C@H](O)O[C@H](CO)[C@H](O)[C@@H]1…`
ZINC8602542	0.708	293.3 Da LogP -2.58 TPSA 145.6	✓ Ro5	✓ Clean	`CC(=O)N[C@H]1[C@H](O[C@H](C)C(=O)O)[C@@H](O)[C@…`
ZINC1580161	0.647	208.3 Da LogP -0.33 TPSA 57.2	✓ Ro5	✓ Clean	`COCCOCCOCCOCCO`
ZINC16052118	0.647	340.4 Da LogP -0.28 TPSA 84.8	✓ Ro5	✓ Clean	`COCCOCCOCCOCCOCCOCCOCCO`
ZINC16052257	0.647	384.5 Da LogP -0.26 TPSA 94.1	✓ Ro5	✓ Clean	`COCCOCCOCCOCCOCCOCCOCCOCCO`
ZINC34317654	0.647	472.6 Da LogP -0.23 TPSA 112.5	1 viol.	✓ Clean	`COCCOCCOCCOCCOCCOCCOCCOCCOCCOCCO`
ZINC44076059	0.647	428.5 Da LogP -0.24 TPSA 103.3	✓ Ro5	✓ Clean	`COCCOCCOCCOCCOCCOCCOCCOCCOCCO`
ZINC5210101	0.647	252.3 Da LogP -0.31 TPSA 66.4	✓ Ro5	✓ Clean	`COCCOCCOCCOCCOCCO`
ZINC5997860	0.647	296.4 Da LogP -0.29 TPSA 75.6	✓ Ro5	✓ Clean	`COCCOCCOCCOCCOCCOCCO`
ZINC13543977	0.628	301.3 Da LogP -3.25 TPSA 162.6	✓ Ro5	✓ Clean	`CC(=O)N[C@H]1[C@@H](O)O[C@H](COS(=O)(=O)O)[C@H]…`
ZINC13543979	0.628	301.3 Da LogP -3.25 TPSA 162.6	✓ Ro5	✓ Clean	`CC(=O)N[C@H]1[C@@H](O)O[C@H](COS(=O)(=O)O)[C@@H…`
ZINC4096329	0.628	301.3 Da LogP -3.25 TPSA 162.6	✓ Ro5	✓ Clean	`CC(=O)N[C@H]1[C@H](O)O[C@H](COS(=O)(=O)O)[C@@H]…`
ZINC4096360	0.628	301.3 Da LogP -3.25 TPSA 162.6	✓ Ro5	✓ Clean	`CC(=O)N[C@H]1[C@H](O)O[C@H](COS(=O)(=O)O)[C@H](…`
ZINC12504154	0.622	230.1 Da LogP -2.47 TPSA 136.7	✓ Ro5	✓ Clean	`O=P(O)(O)OC[C@H]1O[C@H](O)[C@@H](O)[C@@H]1O`
ZINC1532546	0.622	230.1 Da LogP -2.47 TPSA 136.7	✓ Ro5	✓ Clean	`O=P(O)(O)OC[C@@H]1O[C@H](O)[C@@H](O)[C@H]1O`
ZINC4096190	0.622	230.1 Da LogP -2.47 TPSA 136.7	✓ Ro5	✓ Clean	`O=P(O)(O)OC[C@H]1O[C@H](O)[C@H](O)[C@@H]1O`
ZINC4228241	0.622	230.1 Da LogP -2.47 TPSA 136.7	✓ Ro5	✓ Clean	`O=P(O)(O)OC[C@H]1O[C@@H](O)[C@H](O)[C@@H]1O`
ZINC4521831	0.622	230.1 Da LogP -2.47 TPSA 136.7	✓ Ro5	✓ Clean	`O=P(O)(O)OC[C@H]1O[C@@H](O)[C@@H](O)[C@@H]1O`
ZINC1042045	0.615	221.2 Da LogP -3.08 TPSA 119.3	✓ Ro5	✓ Clean	`CC(=O)N[C@@H]1[C@H](O)[C@H](O)[C@H](CO)O[C@H]1O`
ZINC16124914	0.615	221.2 Da LogP -3.08 TPSA 119.3	✓ Ro5	✓ Clean	`CC(=O)N[C@@H]1[C@H](O)O[C@H](CO)[C@H](O)[C@@H]1O`
ZINC2562219	0.615	221.2 Da LogP -3.08 TPSA 119.3	✓ Ro5	✓ Clean	`CC(=O)N[C@H]1[C@@H](O)O[C@H](CO)[C@H](O)[C@@H]1O`
ZINC3860151	0.615	221.2 Da LogP -3.08 TPSA 119.3	✓ Ro5	✓ Clean	`CC(=O)N[C@H]1[C@@H](O)O[C@H](CO)[C@@H](O)[C@@H]…`
ZINC3870075	0.615	221.2 Da LogP -3.08 TPSA 119.3	✓ Ro5	✓ Clean	`CC(=O)N[C@H]1[C@@H](O)O[C@@H](CO)[C@@H](O)[C@H]…`
ZINC3983907	0.615	221.2 Da LogP -3.08 TPSA 119.3	✓ Ro5	✓ Clean	`CC(=O)N[C@H]1[C@H](O)O[C@H](CO)[C@@H](O)[C@@H]1O`
ZINC4228290	0.615	221.2 Da LogP -3.08 TPSA 119.3	✓ Ro5	✓ Clean	`CC(=O)N[C@@H]1[C@H](O)O[C@H](CO)[C@@H](O)[C@@H]…`
ZINC4293686	0.615	221.2 Da LogP -3.08 TPSA 119.3	✓ Ro5	✓ Clean	`CC(=O)N[C@H]1[C@H](O)[C@@H](O)[C@@H](CO)O[C@H]1O`
ZINC4301186	0.615	221.2 Da LogP -3.08 TPSA 119.3	✓ Ro5	✓ Clean	`CC(=O)N[C@@H]1[C@@H](O)O[C@H](CO)[C@H](O)[C@@H]…`
ZINC5227360	0.615	221.2 Da LogP -3.08 TPSA 119.3	✓ Ro5	✓ Clean	`CC(=O)N[C@H]1[C@H](O)[C@H](O)[C@@H](CO)O[C@H]1O`
ZINC5883957	0.615	221.2 Da LogP -3.08 TPSA 119.3	✓ Ro5	✓ Clean	`CC(=O)N[C@@H]1[C@H](O)[C@H](O)[C@@H](CO)O[C@H]1O`
ZINC5883978	0.615	221.2 Da LogP -3.08 TPSA 119.3	✓ Ro5	✓ Clean	`CC(=O)N[C@H]1[C@H](O)O[C@@H](CO)[C@H](O)[C@@H]1O`
ZINC895332	0.615	221.2 Da LogP -3.08 TPSA 119.3	✓ Ro5	✓ Clean	`CC(=O)N[C@H]1[C@@H](O)O[C@@H](CO)[C@H](O)[C@H]1O`
ZINC901459	0.615	221.2 Da LogP -3.08 TPSA 119.3	✓ Ro5	✓ Clean	`CC(=O)N[C@@H]1[C@H](O)[C@@H](O)[C@@H](CO)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.