Protein profile

VK055_3414

bacterial regulatory helix-turn-helix, lysR family protein

Genome: KpATCC43816

Gene: AIK81972.1 Structure source: AlphaFold + ColabFold UniProt A0A0H3GXK9

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Amino acids 396

Annotations 4

Features 32

PDB binders 8

Druggability 0.728

Overview

Basic information about this protein and its source genome.

Accession: VK055_3414
Assembly: Klebsiella pneumoniae subsp. pneumoniae strain ATCC 43816 KPPR1, complete genome
Gene: AIK81972.1
Status: annotated
Amino acids: 396
Structure source: AlphaFold + ColabFold

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:0005829 The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes. 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 (%): 38.889
Localization: Cytoplasmic
ColabFold pLDDT: 93.72

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 0.728

Structure A0A0H3GXK9

Pocket Pocket 19

P2Rank 0.569

Structure A0A0H3GXK9

Pocket Pocket 1

ColabFold model

FPocket 0.93 · Pocket 1

P2Rank 0.645 · Pocket 1

Core conservation Conserved core gene

Roary core

CoreCruncher core

Gut microbiome 17 / 4744 genomes with a hit

Normalized 0.004

Sequence

Primary amino-acid sequence viewer.

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

4 GO

Gene Ontology (GO)

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:0005829 The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
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.

32 records

Show feature table

Start	End	DB	Term	Name
97	184	Gene3D	G3DSA:1.10.10.10	-
97	184	InterPro	IPR036388	Winged helix-like DNA-binding domain superfamily
100	158	Pfam	PF00126	Bacterial regulatory helix-turn-helix protein, lysR family
100	158	InterPro	IPR000847	Transcription regulator HTH, LysR
2	59	Pfam	PF00126	Bacterial regulatory helix-turn-helix protein, lysR family
2	59	InterPro	IPR000847	Transcription regulator HTH, LysR
1	18	Phobius	SIGNAL_PEPTIDE	Signal peptide region
2	76	SUPERFAMILY	SSF46785	Winged helix DNA-binding domain
2	76	InterPro	IPR036390	Winged helix DNA-binding domain superfamily
2	89	PANTHER	PTHR30419	HTH-TYPE TRANSCRIPTIONAL REGULATOR YBHD
1	55	ProSiteProfiles	PS50931	LysR-type HTH domain profile.
1	55	InterPro	IPR000847	Transcription regulator HTH, LysR
97	154	ProSiteProfiles	PS50931	LysR-type HTH domain profile.
97	154	InterPro	IPR000847	Transcription regulator HTH, LysR
1	4	Phobius	SIGNAL_PEPTIDE_N_REGION	N-terminal region of a signal peptide.
184	390	Pfam	PF03466	LysR substrate binding domain
184	390	InterPro	IPR005119	LysR, substrate-binding
19	396	Phobius	NON_CYTOPLASMIC_DOMAIN	Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
36	47	PRINTS	PR00039	LysR bacterial regulatory protein HTH signature
36	47	InterPro	IPR000847	Transcription regulator HTH, LysR
26	36	PRINTS	PR00039	LysR bacterial regulatory protein HTH signature
26	36	InterPro	IPR000847	Transcription regulator HTH, LysR
15	26	PRINTS	PR00039	LysR bacterial regulatory protein HTH signature
15	26	InterPro	IPR000847	Transcription regulator HTH, LysR
5	13	Phobius	SIGNAL_PEPTIDE_H_REGION	Hydrophobic region of a signal peptide.
188	395	Gene3D	G3DSA:3.40.190.290	-
14	18	Phobius	SIGNAL_PEPTIDE_C_REGION	C-terminal region of a signal peptide.
92	207	SUPERFAMILY	SSF46785	Winged helix DNA-binding domain
92	207	InterPro	IPR036390	Winged helix DNA-binding domain superfamily
185	393	SUPERFAMILY	SSF53850	Periplasmic binding protein-like II
1	76	Gene3D	G3DSA:1.10.10.10	-
1	76	InterPro	IPR036388	Winged helix-like DNA-binding domain superfamily

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_A0A0H3GXK9	AlphaFold	—	—	full sequence	—	Viewing
ColabFold VK055_3414	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
19				0.728
13				0.235

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	7.05	0.365
2	2.04	0.045
3	1.98	0.042
4	0.76	0.002

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				0.93

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	9.07	0.486
2	4.39	0.184
3	2.42	0.065
4	1.46	0.02
5	1.06	0.007

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.

58 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
1PS	6G1B	Q8NP91	201.2 Da LogP -0.09 TPSA 61.1	✓ Ro5	✓ Clean	`c1cc[n+](cc1)CCCS(=O)(=O)[O-]`
AKG	5Y2V	P73862	146.1 Da LogP -0.50 TPSA 91.7	✓ Ro5	✓ Clean	`C(CC(=O)O)C(=O)C(=O)O`
FOR	6G1D	Q8NP91	30.0 Da LogP -0.18 TPSA 17.1	✓ Ro5	✓ Clean	`C=O`
PEO	6G1B	Q8NP91	34.0 Da LogP 0.02 TPSA 40.5	✓ Ro5	✓ Clean	`OO`
PEU	2Y7P	Q7WT50	1221.5 Da LogP 0.06 TPSA 269.4	2 viol.	✓ Clean	`COCCOCCOCCOCCOCCOCCOCCOCCOCCOCCOCCOCCOCCOCCOCCO…`
SAL	2Y7K	Q7WT50	138.1 Da LogP 1.09 TPSA 57.5	✓ Ro5	✓ Clean	`c1ccc(c(c1)C(=O)O)O`
SKM	5TED	Q8Y9N7	174.2 Da LogP -1.52 TPSA 98.0	✓ Ro5	✓ Clean	`C1[C@H]([C@@H]([C@@H](C=C1C(=O)O)O)O)O`
TSU	3FXU	P94678	172.2 Da LogP 1.24 TPSA 54.4	✓ Ro5	✓ Clean	`Cc1ccc(cc1)S(=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
ZINC1580161	1.000	208.3 Da LogP -0.33 TPSA 57.2	✓ Ro5	✓ Clean	`COCCOCCOCCOCCO`
ZINC16052118	1.000	340.4 Da LogP -0.28 TPSA 84.8	✓ Ro5	✓ Clean	`COCCOCCOCCOCCOCCOCCOCCO`
ZINC16052257	1.000	384.5 Da LogP -0.26 TPSA 94.1	✓ Ro5	✓ Clean	`COCCOCCOCCOCCOCCOCCOCCOCCO`
ZINC34317654	1.000	472.6 Da LogP -0.23 TPSA 112.5	1 viol.	✓ Clean	`COCCOCCOCCOCCOCCOCCOCCOCCOCCOCCO`
ZINC44076059	1.000	428.5 Da LogP -0.24 TPSA 103.3	✓ Ro5	✓ Clean	`COCCOCCOCCOCCOCCOCCOCCOCCOCCO`
ZINC5210101	1.000	252.3 Da LogP -0.31 TPSA 66.4	✓ Ro5	✓ Clean	`COCCOCCOCCOCCOCCO`
ZINC5997860	1.000	296.4 Da LogP -0.29 TPSA 75.6	✓ Ro5	✓ Clean	`COCCOCCOCCOCCOCCOCCO`
ZINC34564963	0.900	248.3 Da LogP 2.91 TPSA 54.4	✓ Ro5	✓ Clean	`Cc1ccc(-c2ccc(S(=O)(=O)O)cc2)cc1`
ZINC575419714	0.727	312.4 Da LogP 0.42 TPSA 66.4	✓ Ro5	✓ Clean	`COCCOCCOCCSCCOCCOCCO`
ZINC6093151	0.722	238.2 Da LogP 0.18 TPSA 108.7	✓ Ro5	✓ Clean	`O=S(=O)(O)c1ccc(S(=O)(=O)O)cc1`
ZINC115163232	0.700	222.3 Da LogP 0.07 TPSA 57.2	✓ Ro5	✓ Clean	`COCCOCCOCCOCCCO`
ZINC1866983	0.700	314.3 Da LogP 1.85 TPSA 108.7	✓ Ro5	✓ Clean	`O=S(=O)(O)c1ccc(-c2ccc(S(=O)(=O)O)cc2)cc1`
ZINC258837490	0.700	354.4 Da LogP 0.11 TPSA 84.8	✓ Ro5	✓ Clean	`COCCOCCOCCOCCOCCOCCOCCCO`
ZINC12501520	0.688	458.5 Da LogP -0.88 TPSA 123.5	1 viol.	✓ Clean	`OCCOCCOCCOCCOCCOCCOCCOCCOCCOCCO`
ZINC1692489	0.688	222.3 Da LogP 0.33 TPSA 46.2	✓ Ro5	✓ Clean	`COCCOCCOCCOCCOC`
ZINC3874716	0.688	414.5 Da LogP -0.90 TPSA 114.3	✓ Ro5	✓ Clean	`OCCOCCOCCOCCOCCOCCOCCOCCOCCO`
ZINC4283769	0.688	238.3 Da LogP -0.96 TPSA 77.4	✓ Ro5	✓ Clean	`OCCOCCOCCOCCOCCO`
ZINC4521548	0.688	282.3 Da LogP -0.95 TPSA 86.6	✓ Ro5	✓ Clean	`OCCOCCOCCOCCOCCOCCO`
ZINC4530388	0.688	266.3 Da LogP 0.35 TPSA 55.4	✓ Ro5	✓ Clean	`COCCOCCOCCOCCOCCOC`
ZINC5178829	0.688	326.4 Da LogP -0.93 TPSA 95.8	✓ Ro5	✓ Clean	`OCCOCCOCCOCCOCCOCCOCCO`
ZINC5178830	0.688	370.4 Da LogP -0.91 TPSA 105.1	✓ Ro5	✓ Clean	`OCCOCCOCCOCCOCCOCCOCCOCCO`
ZINC5701172	0.688	310.4 Da LogP 0.36 TPSA 64.6	✓ Ro5	✓ Clean	`COCCOCCOCCOCCOCCOCCOC`
ZINC5997861	0.688	398.5 Da LogP 0.40 TPSA 83.1	✓ Ro5	✓ Clean	`COCCOCCOCCOCCOCCOCCOCCOCCOC`
ZINC575432150	0.667	344.4 Da LogP -0.89 TPSA 100.5	✓ Ro5	✓ Clean	`COCCOCCOCCS(=O)(=O)CCOCCOCCO`
ZINC1857524240	0.652	207.3 Da LogP -0.75 TPSA 60.0	✓ Ro5	✓ Clean	`COCCNCCOCCOCCO`
ZINC400143	0.652	214.2 Da LogP 2.76 TPSA 57.5	✓ Ro5	✓ Clean	`O=C(O)c1ccccc1-c1ccccc1O`
ZINC38392758	0.650	242.2 Da LogP 2.16 TPSA 74.6	✓ Ro5	Alert	`O=C(C(=O)c1ccccc1O)c1ccccc1O`
ZINC404363	0.650	214.2 Da LogP 2.33 TPSA 57.5	✓ Ro5	✓ Clean	`O=C(c1ccccc1O)c1ccccc1O`
ZINC4521819	0.643	202.3 Da LogP 0.25 TPSA 58.3	✓ Ro5	✓ Clean	`O=S(=O)(O)CCC[n+]1ccccc1`
ZINC82548310	0.636	236.3 Da LogP 0.34 TPSA 88.5	✓ Ro5	✓ Clean	`CS(=O)(=O)c1ccc(S(=O)(=O)O)cc1`
ZINC105146	0.619	242.2 Da LogP 2.75 TPSA 74.6	✓ Ro5	✓ Clean	`O=C(O)c1ccccc1-c1ccccc1C(=O)O`
ZINC133397	0.619	246.3 Da LogP 3.14 TPSA 34.1	✓ Ro5	✓ Clean	`Cc1ccc(S(=O)(=O)c2ccc(C)cc2)cc1`
ZINC34279126	0.615	222.3 Da LogP 2.39 TPSA 54.4	✓ Ro5	✓ Clean	`Cc1ccc2cc(S(=O)(=O)O)ccc2c1`
ZINC36294287	0.607	248.3 Da LogP 2.91 TPSA 54.4	✓ Ro5	✓ Clean	`Cc1cccc(-c2ccc(S(=O)(=O)O)cc2)c1`
ZINC5650743	0.600	222.3 Da LogP 0.07 TPSA 57.2	✓ Ro5	✓ Clean	`CCOCCOCCOCCOCCO`
ZINC6403917	0.600	354.4 Da LogP 0.11 TPSA 84.8	✓ Ro5	✓ Clean	`CCOCCOCCOCCOCCOCCOCCOCCO`
ZINC2062	0.593	258.2 Da LogP 2.31 TPSA 83.8	✓ Ro5	✓ Clean	`O=C(Oc1ccccc1C(=O)O)c1ccccc1O`
ZINC4831627	0.593	370.5 Da LogP -0.21 TPSA 76.0	✓ Ro5	✓ Clean	`O=S(=O)(CC[n+]1ccccc1)CCS(=O)(=O)CC[n+]1ccccc1`
ZINC116078641	0.583	222.2 Da LogP -0.80 TPSA 74.2	✓ Ro5	✓ Clean	`COC(=O)COCCOCCOCCO`
ZINC1565641	0.583	214.3 Da LogP 2.23 TPSA 54.4	✓ Ro5	✓ Clean	`CC(C)(C)c1ccc(S(=O)(=O)O)cc1`
ZINC1661217	0.583	234.3 Da LogP 2.60 TPSA 54.4	✓ Ro5	✓ Clean	`O=S(=O)(O)c1ccc(-c2ccccc2)cc1`
ZINC1857790631	0.583	280.3 Da LogP -0.39 TPSA 83.5	✓ Ro5	✓ Clean	`COC(=O)CCOCCOCCOCCOCCO`
ZINC196151418	0.583	266.3 Da LogP -0.78 TPSA 83.5	✓ Ro5	✓ Clean	`COC(=O)COCCOCCOCCOCCO`
ZINC202958272	0.583	236.3 Da LogP -0.41 TPSA 74.2	✓ Ro5	✓ Clean	`COC(=O)CCOCCOCCOCCO`
ZINC34111591	0.583	207.3 Da LogP -1.06 TPSA 62.2	✓ Ro5	✓ Clean	`COCCOCCN(CCO)CCO`
ZINC642881862	0.583	324.4 Da LogP -0.38 TPSA 92.7	✓ Ro5	✓ Clean	`COC(=O)CCOCCOCCOCCOCCOCCO`
ZINC82369423	0.583	217.0 Da LogP 1.85 TPSA 57.5	✓ Ro5	✓ Clean	`O=C(O)c1cccc(O)c1Br`
ZINC95713705	0.583	264.0 Da LogP 1.70 TPSA 57.5	✓ Ro5	✓ Clean	`O=C(O)c1cccc(O)c1I`
ZINC1669673	0.577	206.7 Da LogP 1.90 TPSA 54.4	✓ Ro5	✓ Clean	`Cc1ccc(S(=O)(=O)O)cc1Cl`
ZINC39194529	0.577	214.2 Da LogP 2.76 TPSA 57.5	✓ Ro5	✓ Clean	`O=C(O)c1ccc(-c2ccccc2)cc1O`

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.