Protein profile

KP13_04516

Pca regulon regulatory protein

Genome: KpKP13

Gene: AHE44392.1 pcaR Structure source: AlphaFold + ColabFold UniProt A0A0H3GYD2

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Amino acids 298

Annotations 4

Features 18

PDB binders 4

Druggability 0.514

Overview

Basic information about this protein and its source genome.

Accession: KP13_04516
Assembly: Klebsiella pneumoniae subsp. pneumoniae Kp13, complete sequence
Gene: AHE44392.1 pcaR
Status: annotated
Amino acids: 298
Structure source: AlphaFold + ColabFold

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). 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:0045892 Any process that stops, prevents, or reduces the frequency, rate or extent of cellular DNA-templated transcription.

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 (%): 0.0
Localization: Cytoplasmic
ColabFold pLDDT: 83.21

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 0.514

Structure A0A0H3GYD2

Pocket Pocket 14

P2Rank 0.667

Structure A0A0H3GYD2

Pocket Pocket 1

ColabFold model

FPocket 0.942 · Pocket 24

P2Rank 0.721 · Pocket 1

Core conservation Conserved core gene

Roary core

CoreCruncher core

Gut microbiome 30 / 4744 genomes with a hit

Normalized 0.006

Sequence

Primary amino-acid sequence viewer.

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

4 GO

Gene Ontology (GO)

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).
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:0045892 Any process that stops, prevents, or reduces the frequency, rate or extent of cellular DNA-templated transcription.

Sequence Features

Domain/signature hits from InterPro and related databases.

18 records

Show feature table

Start	End	DB	Term	Name
56	104	Pfam	PF09339	IclR helix-turn-helix domain
56	104	InterPro	IPR005471	Transcription regulator IclR, N-terminal
116	298	ProSiteProfiles	PS51078	IclR effector binding domain profile.
116	298	InterPro	IPR014757	Transcription regulator IclR, C-terminal
174	296	Pfam	PF01614	Bacterial transcriptional regulator
174	296	InterPro	IPR014757	Transcription regulator IclR, C-terminal
54	115	ProSiteProfiles	PS51077	IclR-type HTH domain profile.
54	115	InterPro	IPR005471	Transcription regulator IclR, N-terminal
54	143	SMART	SM00346	iclrneu
54	143	InterPro	IPR005471	Transcription regulator IclR, N-terminal
120	298	SUPERFAMILY	SSF55781	GAF domain-like
124	298	Gene3D	G3DSA:3.30.450.40	-
124	298	InterPro	IPR029016	GAF-like domain superfamily
44	297	PANTHER	PTHR30136	HELIX-TURN-HELIX TRANSCRIPTIONAL REGULATOR, ICLR FAMILY
56	125	SUPERFAMILY	SSF46785	Winged helix DNA-binding domain
56	125	InterPro	IPR036390	Winged helix DNA-binding domain superfamily
46	123	Gene3D	G3DSA:1.10.10.10	-
46	123	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_A0A0H3GYD2	AlphaFold	—	—	full sequence	—	Viewing
ColabFold KP13_04516	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
14				0.514

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	Sticks	Spheres	Surfaces	Score	Probability	Labels	Zoom	Positions
1				9.38	0.504

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
24				0.942

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	Sticks	Spheres	Surfaces	Score	Probability	Labels	Zoom	Positions
1				10.31	0.554

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
3HB	5HPI	Q43992	138.1 Da LogP 1.09 TPSA 57.5	✓ Ro5	✓ Clean	`c1cc(cc(c1)O)C(=O)O`
GOA	2O99	P16528	76.1 Da LogP -0.94 TPSA 57.5	✓ Ro5	✓ Clean	`C(C(=O)O)O`
PHB	5W1E	Q9Z4X2	138.1 Da LogP 1.09 TPSA 57.5	✓ Ro5	✓ Clean	`c1cc(ccc1C(=O)O)O`
PYR	2O9A	P16528	88.1 Da LogP -0.34 TPSA 54.4	✓ Ro5	✓ Clean	`CC(=O)C(=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
ZINC389804	0.842	214.2 Da LogP 2.76 TPSA 57.5	✓ Ro5	✓ Clean	`O=C(O)c1ccc(-c2ccc(O)cc2)cc1`
ZINC33246180	0.727	242.2 Da LogP 3.51 TPSA 82.2	✓ Ro5	Alert	`O=C(O)c1ccc(N=Nc2ccc(O)cc2)cc1`
ZINC3896282	0.727	242.2 Da LogP 3.51 TPSA 82.2	✓ Ro5	Alert	`O=C(O)c1ccc(/N=N/c2ccc(O)cc2)cc1`
ZINC392302	0.727	230.2 Da LogP 2.88 TPSA 66.8	✓ Ro5	✓ Clean	`O=C(O)c1ccc(Oc2ccc(O)cc2)cc1`
ZINC39410336	0.727	242.2 Da LogP 2.16 TPSA 74.6	✓ Ro5	Alert	`O=C(C(=O)c1cccc(O)c1)c1cccc(O)c1`
ZINC289893	0.696	278.3 Da LogP 1.92 TPSA 91.7	✓ Ro5	✓ Clean	`O=C(O)c1ccc(S(=O)(=O)c2ccc(O)cc2)cc1`
ZINC114185151	0.667	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`
ZINC2924369	0.667	242.2 Da LogP 2.16 TPSA 74.6	✓ Ro5	Alert	`O=C(C(=O)c1ccc(O)cc1)c1ccc(O)cc1`
ZINC3156317	0.640	258.2 Da LogP 2.31 TPSA 83.8	✓ Ro5	✓ Clean	`O=C(O)c1ccc(OC(=O)c2ccc(O)cc2)cc1`
ZINC4903179	0.640	257.2 Da LogP 2.34 TPSA 86.6	✓ Ro5	✓ Clean	`O=C(O)c1ccc(NC(=O)c2ccc(O)cc2)cc1`
ZINC134079	0.632	242.2 Da LogP 2.75 TPSA 74.6	✓ Ro5	✓ Clean	`O=C(O)c1ccc(-c2ccc(C(=O)O)cc2)cc1`
ZINC1640789	0.632	374.3 Da LogP 3.55 TPSA 108.7	✓ Ro5	✓ Clean	`O=C(O)c1ccc(C(=O)c2ccc(C(=O)c3ccc(C(=O)O)cc3)cc…`
ZINC2146859	0.632	270.2 Da LogP 2.31 TPSA 91.7	✓ Ro5	✓ Clean	`O=C(O)c1ccc(C(=O)c2ccc(C(=O)O)cc2)cc1`
ZINC28449	0.632	214.2 Da LogP 2.33 TPSA 57.5	✓ Ro5	✓ Clean	`O=C(c1ccc(O)cc1)c1ccc(O)cc1`
ZINC3147211	0.632	318.3 Da LogP 4.42 TPSA 74.6	✓ Ro5	✓ Clean	`O=C(O)c1ccc(-c2ccc(-c3ccc(C(=O)O)cc3)cc2)cc1`
ZINC332365	0.632	318.3 Da LogP 3.56 TPSA 74.6	✓ Ro5	✓ Clean	`O=C(c1ccc(O)cc1)c1ccc(C(=O)c2ccc(O)cc2)cc1`
ZINC1705144	0.619	226.2 Da LogP 2.46 TPSA 54.4	✓ Ro5	Alert	`O=C(C(=O)c1ccc(O)cc1)c1ccccc1`
ZINC65347101	0.594	215.2 Da LogP 2.15 TPSA 70.4	✓ Ro5	✓ Clean	`O=C(O)c1ccnc(-c2cccc(O)c2)c1`
ZINC6338454	0.593	268.3 Da LogP 2.99 TPSA 74.6	✓ Ro5	✓ Clean	`O=C(O)c1ccc(/C=C/C(=O)c2ccc(O)cc2)cc1`
ZINC65340137	0.583	258.2 Da LogP 2.46 TPSA 94.8	✓ Ro5	✓ Clean	`O=C(O)c1cc(C(=O)O)cc(-c2ccc(O)cc2)c1`
ZINC167226	0.577	248.0 Da LogP 1.99 TPSA 37.3	✓ Ro5	✓ Clean	`O=C(O)c1cccc(I)c1`
ZINC404749	0.577	201.0 Da LogP 2.15 TPSA 37.3	✓ Ro5	✓ Clean	`O=C(O)c1cccc(Br)c1`
ZINC409186	0.577	226.2 Da LogP 2.62 TPSA 54.4	✓ Ro5	✓ Clean	`O=C(O)c1cccc(C(=O)c2ccccc2)c1`
ZINC167246	0.571	248.0 Da LogP 1.99 TPSA 37.3	✓ Ro5	✓ Clean	`O=C(O)c1ccc(I)cc1`
ZINC3269660	0.571	254.2 Da LogP 2.45 TPSA 71.4	✓ Ro5	Alert	`O=C(O)c1ccc(C(=O)C(=O)c2ccccc2)cc1`
ZINC34573580	0.571	496.5 Da LogP 4.86 TPSA 149.2	✓ Ro5	✓ Clean	`O=C(O)c1ccc(C(c2ccc(C(=O)O)cc2)(c2ccc(C(=O)O)cc…`
ZINC388063	0.571	201.0 Da LogP 2.15 TPSA 37.3	✓ Ro5	✓ Clean	`O=C(O)c1ccc(Br)cc1`
ZINC896125	0.571	246.2 Da LogP 1.74 TPSA 98.0	✓ Ro5	✓ Clean	`O=C(c1cccc(O)c1)c1c(O)cc(O)cc1O`
ZINC2528073	0.567	213.2 Da LogP 2.64 TPSA 49.3	✓ Ro5	✓ Clean	`O=C(Nc1ccccc1)c1cccc(O)c1`
ZINC2558112	0.567	214.2 Da LogP 2.61 TPSA 46.5	✓ Ro5	✓ Clean	`O=C(Oc1ccccc1)c1cccc(O)c1`
ZINC38167261	0.567	208.2 Da LogP 0.62 TPSA 91.7	✓ Ro5	✓ Clean	`O=C(O)C(=O)CC(=O)c1cccc(O)c1`
ZINC6732169	0.567	208.2 Da LogP 0.94 TPSA 94.8	✓ Ro5	✓ Clean	`O=C(O)C(=O)/C=C(\O)c1cccc(O)c1`
ZINC571052	0.559	241.2 Da LogP 2.84 TPSA 69.9	✓ Ro5	✓ Clean	`O=C(O)c1cccc(/N=C/c2cccc(O)c2)c1`
ZINC1687604	0.552	214.2 Da LogP 2.33 TPSA 57.5	✓ Ro5	✓ Clean	`O=C(c1cccc(O)c1)c1ccccc1O`
ZINC1812572	0.552	300.3 Da LogP 1.26 TPSA 98.7	✓ Ro5	✓ Clean	`O=C(NCCNC(=O)c1cccc(O)c1)c1cccc(O)c1`
ZINC5234593	0.552	293.3 Da LogP 1.89 TPSA 103.7	✓ Ro5	Alert	`O=C(O)c1ccc(S(=O)(=O)Nc2ccc(O)cc2)cc1`
ZINC102314234	0.548	210.3 Da LogP 2.14 TPSA 57.5	✓ Ro5	✓ Clean	`C/C(=C(\S)C(=O)O)c1cccc(O)c1`
ZINC115778137	0.548	216.2 Da LogP 1.55 TPSA 83.3	✓ Ro5	✓ Clean	`O=C(O)c1cccc(-c2ncc(O)cn2)c1`
ZINC20266271	0.548	233.3 Da LogP 2.80 TPSA 40.5	✓ Ro5	✓ Clean	`O=C(c1cccc(O)c1)N1CCCCCCC1`
ZINC6760627	0.548	205.3 Da LogP 2.02 TPSA 40.5	✓ Ro5	✓ Clean	`O=C(c1cccc(O)c1)N1CCCCC1`
ZINC13375284	0.545	270.2 Da LogP 3.50 TPSA 99.3	✓ Ro5	Alert	`O=C(O)c1ccc(N=Nc2ccc(C(=O)O)cc2)cc1`
ZINC156520	0.545	268.3 Da LogP 3.25 TPSA 74.6	✓ Ro5	✓ Clean	`O=C(O)c1ccc(/C=C/c2ccc(C(=O)O)cc2)cc1`
ZINC1651850	0.545	270.3 Da LogP 2.87 TPSA 74.6	✓ Ro5	✓ Clean	`O=C(O)c1ccc(CCc2ccc(C(=O)O)cc2)cc1`
ZINC1759946	0.545	256.3 Da LogP 2.67 TPSA 74.6	✓ Ro5	✓ Clean	`O=C(O)c1ccc(Cc2ccc(C(=O)O)cc2)cc1`
ZINC1857524265	0.545	268.3 Da LogP 3.25 TPSA 74.6	✓ Ro5	✓ Clean	`O=C(O)c1ccc(C=Cc2ccc(C(=O)O)cc2)cc1`
ZINC241160	0.545	258.2 Da LogP 2.88 TPSA 83.8	✓ Ro5	✓ Clean	`O=C(O)c1ccc(Oc2ccc(C(=O)O)cc2)cc1`
ZINC2504355	0.545	226.2 Da LogP 2.62 TPSA 54.4	✓ Ro5	✓ Clean	`O=C(O)c1ccc(C(=O)c2ccccc2)cc1`
ZINC4792283	0.545	268.3 Da LogP 3.25 TPSA 74.6	✓ Ro5	✓ Clean	`O=C(O)c1ccc(/C=C\c2ccc(C(=O)O)cc2)cc1`
ZINC8418684	0.545	257.2 Da LogP 2.83 TPSA 86.6	✓ Ro5	✓ Clean	`O=C(O)c1ccc(Nc2ccc(C(=O)O)cc2)cc1`
ZINC96024941	0.545	366.4 Da LogP 3.88 TPSA 74.6	✓ Ro5	✓ Clean	`O=C(O)c1ccc(C#Cc2ccc(C#Cc3ccc(C(=O)O)cc3)cc2)cc1`

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.