Protein profile

KP13_05488

AraC family transcriptional regulator

Genome: KpKP13

Gene: AHE44493.1 Structure source: AlphaFold + ColabFold UniProt A0A9Q8CCE8

Export view

Amino acids 351

Annotations 3

Features 25

PDB binders 2

Druggability 0.634

Overview

Basic information about this protein and its source genome.

Accession: KP13_05488
Assembly: Klebsiella pneumoniae subsp. pneumoniae Kp13, complete sequence
Gene: AHE44493.1
Status: annotated
Amino acids: 351
Structure source: AlphaFold + ColabFold

GO:0043565 Binding to DNA of a specific nucleotide composition, e.g. GC-rich DNA binding, or with a specific sequence motif or type of DNA e.g. promotor binding or rDNA binding. GO:0006355 Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription. 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.

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: Unknown
ColabFold pLDDT: 90.28

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 0.634

Structure A0A9Q8CCE8

Pocket Pocket 1

P2Rank 0.244

Structure A0A9Q8CCE8

Pocket Pocket 1

ColabFold model

FPocket 0.681 · Pocket 4

P2Rank 0.16 · Pocket 1

Core conservation Accessory gene

Roary accessory

CoreCruncher accessory

Gut microbiome 6 / 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.

3 GO

Gene Ontology (GO)

GO:0043565 Binding to DNA of a specific nucleotide composition, e.g. GC-rich DNA binding, or with a specific sequence motif or type of DNA e.g. promotor binding or rDNA binding.
GO:0006355 Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
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.

Sequence Features

Domain/signature hits from InterPro and related databases.

25 records

Show feature table

Start	End	DB	Term	Name
244	345	ProSiteProfiles	PS01124	Bacterial regulatory proteins, araC family DNA-binding domain profile.
244	345	InterPro	IPR018060	DNA binding HTH domain, AraC-type
20	225	SUPERFAMILY	SSF52317	Class I glutamine amidotransferase-like
20	225	InterPro	IPR029062	Class I glutamine amidotransferase-like
297	339	ProSitePatterns	PS00041	Bacterial regulatory proteins, araC family signature.
297	339	InterPro	IPR018062	HTH domain AraC-type, conserved site
37	351	Phobius	NON_CYTOPLASMIC_DOMAIN	Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
16	232	Gene3D	G3DSA:3.40.50.880	-
16	232	InterPro	IPR029062	Class I glutamine amidotransferase-like
247	346	Gene3D	G3DSA:1.10.10.60	-
1	21	Phobius	SIGNAL_PEPTIDE_N_REGION	N-terminal region of a signal peptide.
1	36	Phobius	SIGNAL_PEPTIDE	Signal peptide region
66	203	Pfam	PF01965	DJ-1/PfpI family
66	203	InterPro	IPR002818	DJ-1/PfpI
296	346	SUPERFAMILY	SSF46689	Homeodomain-like
296	346	InterPro	IPR009057	Homeobox-like domain superfamily
260	343	SMART	SM00342	aracneu4
260	343	InterPro	IPR018060	DNA binding HTH domain, AraC-type
1	36	SignalP_GRAM_NEGATIVE	SignalP-noTM	SignalP-noTM
22	225	CDD	cd03138	GATase1_AraC_2
30	36	Phobius	SIGNAL_PEPTIDE_C_REGION	C-terminal region of a signal peptide.
20	280	PANTHER	PTHR43130	ARAC-FAMILY TRANSCRIPTIONAL REGULATOR
266	345	Pfam	PF12833	Helix-turn-helix domain
266	345	InterPro	IPR018060	DNA binding HTH domain, AraC-type
22	29	Phobius	SIGNAL_PEPTIDE_H_REGION	Hydrophobic region of a signal peptide.

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...

Legend High Medium Low

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_A0A9Q8CCE8	AlphaFold	—	—	full sequence	—	Viewing
ColabFold KP13_05488	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				0.634

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	4.53	0.194
2	3.96	0.157
3	2.1	0.048

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
4				0.681

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	3.24	0.112
2	2.22	0.054
3	2.0	0.043

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.

52 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
NHE	3NOQ	Q4K977	207.3 Da LogP 0.80 TPSA 66.4	✓ Ro5	✓ Clean	`C1CCC(CC1)NCCS(=O)(=O)O`
QCV	6UND	Q4K977	150.1 Da LogP 1.93 TPSA 55.5	✓ Ro5	✓ Clean	`C=Nc1ccc(cc1)N(=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
ZINC1710230	1.000	207.3 Da LogP 0.80 TPSA 66.4	✓ Ro5	✓ Clean	`O=S(=O)(O)CCNC1CCCCC1`
ZINC2004372	0.786	221.3 Da LogP 1.19 TPSA 66.4	✓ Ro5	✓ Clean	`O=S(=O)(O)CCCNC1CCCCC1`
ZINC38364153	0.786	235.3 Da LogP 1.58 TPSA 66.4	✓ Ro5	✓ Clean	`O=S(=O)(O)CCCCNC1CCCCC1`
ZINC1532902	0.700	206.2 Da LogP -0.86 TPSA 132.1	✓ Ro5	✓ Clean	`O=C(O)CC[C@@](O)(CC(=O)O)C(=O)O`
ZINC2018106	0.700	206.2 Da LogP -0.86 TPSA 132.1	✓ Ro5	✓ Clean	`O=C(O)CC[C@](O)(CC(=O)O)C(=O)O`
ZINC100349549	0.667	272.2 Da LogP 3.92 TPSA 111.0	✓ Ro5	Alert	`O=[N+]([O-])c1ccc(/N=N\c2ccc([N+](=O)[O-])cc2)c…`
ZINC13477308	0.667	272.2 Da LogP 3.92 TPSA 111.0	✓ Ro5	Alert	`O=[N+]([O-])c1ccc(/N=N/c2ccc([N+](=O)[O-])cc2)c…`
ZINC3593496	0.652	206.2 Da LogP -1.16 TPSA 121.1	✓ Ro5	✓ Clean	`COC(=O)C[C@@](O)(CC(=O)O)C(=O)O`
ZINC3593497	0.652	206.2 Da LogP -1.16 TPSA 121.1	✓ Ro5	✓ Clean	`COC(=O)C[C@](O)(CC(=O)O)C(=O)O`
ZINC14686440	0.625	436.4 Da LogP -2.64 TPSA 247.9	1 viol.	✓ Clean	`O=C(O)C[C@](O)(CC(=O)NCCCCNC(=O)C[C@@](O)(CC(=O…`
ZINC14686442	0.625	436.4 Da LogP -2.64 TPSA 247.9	1 viol.	✓ Clean	`O=C(O)C[C@@](O)(CC(=O)NCCCCNC(=O)C[C@](O)(CC(=O…`
ZINC14686444	0.625	436.4 Da LogP -2.64 TPSA 247.9	1 viol.	✓ Clean	`O=C(O)C[C@@](O)(CC(=O)NCCCCNC(=O)C[C@@](O)(CC(=…`
ZINC104039967	0.615	288.2 Da LogP 3.43 TPSA 124.7	✓ Ro5	Alert	`O=[N+]([O-])c1ccc(N=[N+]([O-])c2ccc([N+](=O)[O-…`
ZINC13398039	0.577	234.2 Da LogP -0.38 TPSA 121.1	✓ Ro5	✓ Clean	`CC(C)OC(=O)C[C@](O)(CC(=O)O)C(=O)O`
ZINC2528012	0.577	234.2 Da LogP -0.38 TPSA 121.1	✓ Ro5	✓ Clean	`CC(C)OC(=O)C[C@@](O)(CC(=O)O)C(=O)O`
ZINC100172111	0.571	227.2 Da LogP 4.01 TPSA 67.9	✓ Ro5	Alert	`O=[N+]([O-])c1ccc(/N=N\c2ccccc2)cc1`
ZINC18084630	0.571	227.2 Da LogP 4.01 TPSA 67.9	✓ Ro5	Alert	`O=[N+]([O-])c1ccc(/N=N/c2ccccc2)cc1`
ZINC254365173	0.571	227.2 Da LogP 4.01 TPSA 67.9	✓ Ro5	Alert	`O=[N+]([O-])c1ccc(N=Nc2ccccc2)cc1`
ZINC146315135	0.560	204.2 Da LogP 0.86 TPSA 94.8	✓ Ro5	✓ Clean	`CCCCC[C@@](O)(CC(=O)O)C(=O)O`
ZINC146315336	0.560	204.2 Da LogP 0.86 TPSA 94.8	✓ Ro5	✓ Clean	`CCCCC[C@](O)(CC(=O)O)C(=O)O`
ZINC19367005	0.560	224.4 Da LogP 2.83 TPSA 24.1	✓ Ro5	✓ Clean	`C1CCC(NCCNC2CCCCC2)CC1`
ZINC26468763	0.559	243.3 Da LogP -1.35 TPSA 100.5	✓ Ro5	✓ Clean	`O=S(=O)(O)CCN[C@@H]1CCS(=O)(=O)C1`
ZINC26468770	0.559	243.3 Da LogP -1.35 TPSA 100.5	✓ Ro5	✓ Clean	`O=S(=O)(O)CCN[C@H]1CCS(=O)(=O)C1`
ZINC1850353	0.556	206.1 Da LogP -0.86 TPSA 132.1	✓ Ro5	✓ Clean	`O=C(O)CC(O)(CC(=O)O)CC(=O)O`
ZINC5188799	0.556	280.5 Da LogP 4.39 TPSA 24.1	✓ Ro5	✓ Clean	`C(CCCNC1CCCCC1)CCNC1CCCCC1`
ZINC100009138	0.552	243.2 Da LogP 3.72 TPSA 88.1	✓ Ro5	Alert	`O=[N+]([O-])c1ccc(/N=N\c2ccc(O)cc2)cc1`
ZINC100009140	0.552	243.2 Da LogP 3.72 TPSA 88.1	✓ Ro5	Alert	`O=[N+]([O-])c1ccc(/N=N/c2ccc(O)cc2)cc1`
ZINC12405069	0.552	242.2 Da LogP 3.59 TPSA 93.9	✓ Ro5	Alert	`Nc1ccc(N=Nc2ccc([N+](=O)[O-])cc2)cc1`
ZINC254392989	0.552	243.2 Da LogP 3.72 TPSA 88.1	✓ Ro5	Alert	`O=[N+]([O-])c1ccc(N=Nc2ccc(O)cc2)cc1`
ZINC3861520	0.552	242.2 Da LogP 3.59 TPSA 93.9	✓ Ro5	Alert	`Nc1ccc(/N=N/c2ccc([N+](=O)[O-])cc2)cc1`
ZINC4461716	0.552	241.3 Da LogP 4.32 TPSA 67.9	✓ Ro5	Alert	`Cc1ccc(/N=N/c2ccc([N+](=O)[O-])cc2)cc1`
ZINC100838097	0.548	336.3 Da LogP 2.98 TPSA 145.1	✓ Ro5	Alert	`O=[N+]([O-])c1ccc(/N=N/S(=O)(=O)c2ccc([N+](=O)[…`
ZINC1604377	0.542	320.3 Da LogP 4.84 TPSA 86.3	✓ Ro5	✓ Clean	`O=[N+]([O-])c1ccc(-c2ccc(-c3ccc([N+](=O)[O-])cc…`
ZINC1648209	0.542	244.2 Da LogP 3.17 TPSA 86.3	✓ Ro5	✓ Clean	`O=[N+]([O-])c1ccc(-c2ccc([N+](=O)[O-])cc2)cc1`
ZINC100480229	0.533	271.2 Da LogP 3.25 TPSA 98.6	✓ Ro5	✓ Clean	`O=[N+]([O-])c1ccc(/C=N\c2ccc([N+](=O)[O-])cc2)c…`
ZINC12403614	0.533	271.2 Da LogP 3.25 TPSA 98.6	✓ Ro5	✓ Clean	`O=[N+]([O-])c1ccc(/C=N/c2ccc([N+](=O)[O-])cc2)c…`
ZINC254391581	0.533	271.2 Da LogP 3.25 TPSA 98.6	✓ Ro5	✓ Clean	`O=[N+]([O-])c1ccc(C=Nc2ccc([N+](=O)[O-])cc2)cc1`
ZINC39239102	0.533	214.2 Da LogP 1.95 TPSA 72.6	✓ Ro5	✓ Clean	`CS(C)(=O)=Nc1ccc([N+](=O)[O-])cc1`
ZINC2168583	0.529	237.3 Da LogP 0.16 TPSA 86.6	✓ Ro5	✓ Clean	`O=S(=O)(O)C[C@@H](O)CNC1CCCCC1`
ZINC2168584	0.529	237.3 Da LogP 0.16 TPSA 86.6	✓ Ro5	✓ Clean	`O=S(=O)(O)C[C@H](O)CNC1CCCCC1`
ZINC13398014	0.522	220.2 Da LogP -1.07 TPSA 110.1	✓ Ro5	✓ Clean	`COC(=O)CC(O)(CC(=O)OC)C(=O)O`
ZINC3861629	0.522	206.1 Da LogP -1.16 TPSA 121.1	✓ Ro5	✓ Clean	`COC(=O)C(O)(CC(=O)O)CC(=O)O`
ZINC130127586	0.515	260.4 Da LogP 1.38 TPSA 58.2	✓ Ro5	✓ Clean	`O=S(=O)(NCCNC1CCCCCC1)C1CC1`
ZINC78421079	0.515	210.3 Da LogP 1.43 TPSA 41.1	✓ Ro5	✓ Clean	`O=C(NCCNC1CCCCC1)C1CC1`
ZINC104075553	0.500	243.2 Da LogP 3.52 TPSA 81.6	✓ Ro5	Alert	`O=[N+]([O-])c1ccc([N+]([O-])=Nc2ccccc2)cc1`
ZINC1511626	0.500	249.0 Da LogP 2.20 TPSA 43.1	✓ Ro5	✓ Clean	`O=[N+]([O-])c1ccc(I)cc1`
ZINC165485	0.500	301.8 Da LogP 3.04 TPSA 46.2	✓ Ro5	✓ Clean	`O=S(=O)(CCNC1CCCCC1)c1ccc(Cl)cc1`
ZINC17005675	0.500	257.2 Da LogP 4.02 TPSA 77.1	✓ Ro5	Alert	`COc1ccc(/N=N/c2ccc([N+](=O)[O-])cc2)cc1`
ZINC4113982	0.500	270.3 Da LogP 4.08 TPSA 71.1	✓ Ro5	Alert	`CN(C)c1ccc(/N=N/c2ccc([N+](=O)[O-])cc2)cc1`
ZINC60934954	0.500	315.9 Da LogP 3.43 TPSA 46.2	✓ Ro5	✓ Clean	`O=S(=O)(CCNC1CCCCCC1)c1ccc(Cl)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.