Protein profile

KP13_00560

putative HTH-type transcriptional regulator

Genome: KpKP13

Gene: AHE47035.1 Structure source: AlphaFold + ColabFold UniProt A0A0H3GPQ5

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Amino acids 328

Annotations 3

Features 19

PDB binders 4

Druggability 0.447

Overview

Basic information about this protein and its source genome.

Accession: KP13_00560
Assembly: Klebsiella pneumoniae subsp. pneumoniae Kp13, complete sequence
Gene: AHE47035.1
Status: annotated
Amino acids: 328
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: Cytoplasmic
ColabFold pLDDT: 76.25

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 0.447

Structure A0A0H3GPQ5

Pocket Pocket 29

P2Rank 0.632

Structure A0A0H3GPQ5

Pocket Pocket 1

ColabFold model

FPocket 0.115 · Pocket 25

P2Rank 0.146 · Pocket 1

Core conservation Accessory gene

Roary accessory

CoreCruncher accessory

Gut microbiome 49 / 4744 genomes with a hit

Normalized 0.01

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.

19 records

Show feature table

Start	End	DB	Term	Name
229	312	SMART	SM00342	aracneu4
229	312	InterPro	IPR018060	DNA binding HTH domain, AraC-type
214	262	SUPERFAMILY	SSF46689	Homeodomain-like
214	262	InterPro	IPR009057	Homeobox-like domain superfamily
211	262	Gene3D	G3DSA:1.10.10.60	-
89	317	PANTHER	PTHR43280	ARAC-FAMILY TRANSCRIPTIONAL REGULATOR
236	314	Pfam	PF12833	Helix-turn-helix domain
236	314	InterPro	IPR018060	DNA binding HTH domain, AraC-type
265	317	SUPERFAMILY	SSF46689	Homeodomain-like
265	317	InterPro	IPR009057	Homeobox-like domain superfamily
296	312	PRINTS	PR00032	AraC bacterial regulatory protein HTH signature
296	312	InterPro	IPR020449	Transcription regulator HTH, AraC- type
281	296	PRINTS	PR00032	AraC bacterial regulatory protein HTH signature
281	296	InterPro	IPR020449	Transcription regulator HTH, AraC- type
263	319	Gene3D	G3DSA:1.10.10.60	-
216	314	ProSiteProfiles	PS01124	Bacterial regulatory proteins, araC family DNA-binding domain profile.
216	314	InterPro	IPR018060	DNA binding HTH domain, AraC-type
266	308	ProSitePatterns	PS00041	Bacterial regulatory proteins, araC family signature.
266	308	InterPro	IPR018062	HTH domain AraC-type, conserved site

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_A0A0H3GPQ5	AlphaFold	—	—	full sequence	—	Viewing
ColabFold KP13_00560	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
29				0.447

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	7.84	0.416
2	3.53	0.13
3	1.48	0.021
4	1.02	0.006

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				2.59	0.074
2				2.3	0.058

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
70G	5SUW	A5F384	218.3 Da LogP 3.28 TPSA 37.3	✓ Ro5	✓ Clean	`Cc1cccc2c1[C@H](CCC2)CCC(=O)O`
70H	5SUX	Q7BGC0	226.3 Da LogP 3.64 TPSA 37.3	✓ Ro5	✓ Clean	`Cc1cccc2c1c(ccc2)/C=C/CC(=O)O`
BTB	3OOU	Q92A04	209.2 Da LogP -3.01 TPSA 104.4	✓ Ro5	✓ Clean	`C(CO)N(CCO)C(CO)(CO)CO`
PAM	3GBG	A5F384	254.4 Da LogP 5.33 TPSA 37.3	1 viol.	✓ Clean	`CCCCCC\C=C/CCCCCCCC(=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
ZINC1615342	1.000	209.2 Da LogP -3.01 TPSA 104.4	✓ Ro5	✓ Clean	`OCCN(CCO)C(CO)(CO)CO`
ZINC64633397	1.000	226.4 Da LogP 4.55 TPSA 37.3	✓ Ro5	✓ Clean	`CCCCCC/C=C\CCCCCC(=O)O`
ZINC1531062	0.917	226.4 Da LogP 4.55 TPSA 37.3	✓ Ro5	✓ Clean	`CCCC/C=C/CCCCCCCC(=O)O`
ZINC2504617	0.917	240.4 Da LogP 4.94 TPSA 37.3	✓ Ro5	✓ Clean	`CCCC/C=C/CCCCCCCCC(=O)O`
ZINC32786138	0.917	226.4 Da LogP 4.55 TPSA 37.3	✓ Ro5	✓ Clean	`CCCCCCCC/C=C/CCCC(=O)O`
ZINC4529321	0.917	226.4 Da LogP 4.55 TPSA 37.3	✓ Ro5	✓ Clean	`CCCC/C=C\CCCCCCCC(=O)O`
ZINC5260769	0.917	240.4 Da LogP 4.94 TPSA 37.3	✓ Ro5	✓ Clean	`CCCC/C=C\CCCCCCCCC(=O)O`
ZINC31439572	0.778	224.3 Da LogP 4.32 TPSA 37.3	✓ Ro5	✓ Clean	`CCCCC/C=C\C/C=C\CCCC(=O)O`
ZINC198743420	0.750	228.3 Da LogP 2.83 TPSA 74.6	✓ Ro5	✓ Clean	`O=C(O)CCC/C=C\CCCCCC(=O)O`
ZINC1529498	0.739	200.3 Da LogP 3.99 TPSA 37.3	✓ Ro5	✓ Clean	`CCCCCCCCCCCC(=O)O`
ZINC1530417	0.739	228.4 Da LogP 4.77 TPSA 37.3	✓ Ro5	✓ Clean	`CCCCCCCCCCCCCC(=O)O`
ZINC1628119	0.739	214.3 Da LogP 4.38 TPSA 37.3	✓ Ro5	✓ Clean	`CCCCCCCCCCCCC(=O)O`
ZINC33954988	0.719	296.5 Da LogP 4.86 TPSA 57.5	✓ Ro5	✓ Clean	`CCCCC/C=C\C[C@H](O)/C=C/CCCCCCC(=O)O`
ZINC33954989	0.719	296.5 Da LogP 4.86 TPSA 57.5	✓ Ro5	✓ Clean	`CCCCC/C=C\C[C@@H](O)/C=C/CCCCCCC(=O)O`
ZINC33820298	0.714	250.4 Da LogP 4.88 TPSA 37.3	✓ Ro5	✓ Clean	`CCCCC/C=C/C/C=C/C/C=C/CCC(=O)O`
ZINC100079757	0.704	253.4 Da LogP 4.73 TPSA 43.1	✓ Ro5	✓ Clean	`CCCCCC/C=C\CCCCCCCC(N)=O`
ZINC100104940	0.704	210.4 Da LogP 4.66 TPSA 17.1	✓ Ro5	✓ Clean	`CCCCCC/C=C\CCCCC(C)=O`
ZINC104347692	0.704	226.4 Da LogP 4.55 TPSA 37.3	✓ Ro5	✓ Clean	`CCCCCCCCCC/C=C\CC(=O)O`
ZINC1665926	0.704	226.4 Da LogP 4.55 TPSA 37.3	✓ Ro5	✓ Clean	`CCCCCCCCCC/C=C/CC(=O)O`
ZINC85922479	0.704	210.4 Da LogP 4.66 TPSA 17.1	✓ Ro5	✓ Clean	`CCCCCC/C=C/CCCCC(C)=O`
ZINC33822120	0.690	250.4 Da LogP 4.88 TPSA 37.3	✓ Ro5	✓ Clean	`CC/C=C\C/C=C\C/C=C\CCCCCC(=O)O`
ZINC13433851	0.680	200.2 Da LogP 2.05 TPSA 74.6	✓ Ro5	✓ Clean	`O=C(O)CC/C=C/CCCCC(=O)O`
ZINC12496439	0.676	314.5 Da LogP 4.05 TPSA 77.8	✓ Ro5	✓ Clean	`CCCCC/C=C\C[C@@H](O)[C@@H](O)CCCCCCCC(=O)O`
ZINC12496441	0.676	314.5 Da LogP 4.05 TPSA 77.8	✓ Ro5	✓ Clean	`CCCCC/C=C\C[C@H](O)[C@@H](O)CCCCCCCC(=O)O`
ZINC12496444	0.676	314.5 Da LogP 4.05 TPSA 77.8	✓ Ro5	✓ Clean	`CCCCC/C=C\C[C@@H](O)[C@H](O)CCCCCCCC(=O)O`
ZINC12496452	0.676	314.5 Da LogP 4.05 TPSA 77.8	✓ Ro5	✓ Clean	`CCCCC[C@@H](O)[C@@H](O)C/C=C\CCCCCCCC(=O)O`
ZINC12496457	0.676	314.5 Da LogP 4.05 TPSA 77.8	✓ Ro5	✓ Clean	`CCCCC[C@H](O)[C@@H](O)C/C=C\CCCCCCCC(=O)O`
ZINC12496461	0.676	314.5 Da LogP 4.05 TPSA 77.8	✓ Ro5	✓ Clean	`CCCCC[C@@H](O)[C@H](O)C/C=C\CCCCCCCC(=O)O`
ZINC12496465	0.676	314.5 Da LogP 4.05 TPSA 77.8	✓ Ro5	✓ Clean	`CCCCC[C@H](O)[C@H](O)C/C=C\CCCCCCCC(=O)O`
ZINC13336178	0.676	314.5 Da LogP 4.05 TPSA 77.8	✓ Ro5	✓ Clean	`CCCCC/C=C/C[C@@H](O)[C@H](O)CCCCCCCC(=O)O`
ZINC2356452777	0.676	314.5 Da LogP 4.05 TPSA 77.8	✓ Ro5	✓ Clean	`CCCCC[C@H](O)[C@H](O)CC=CCCCCCCCC(=O)O`
ZINC2356452778	0.676	314.5 Da LogP 4.05 TPSA 77.8	✓ Ro5	✓ Clean	`CCCCC[C@@H](O)[C@H](O)CC=CCCCCCCCC(=O)O`
ZINC2356452779	0.676	314.5 Da LogP 4.05 TPSA 77.8	✓ Ro5	✓ Clean	`CCCCC[C@H](O)[C@@H](O)CC=CCCCCCCCC(=O)O`
ZINC2356452780	0.676	314.5 Da LogP 4.05 TPSA 77.8	✓ Ro5	✓ Clean	`CCCCC[C@@H](O)[C@@H](O)CC=CCCCCCCCC(=O)O`
ZINC14512621	0.667	200.3 Da LogP 2.35 TPSA 57.5	✓ Ro5	✓ Clean	`O=C(O)CCCCCCC/C=C/CO`
ZINC31159201	0.667	228.3 Da LogP 2.83 TPSA 74.6	✓ Ro5	✓ Clean	`O=C(O)C/C=C\CCCCCCCC(=O)O`
ZINC102184976	0.657	312.4 Da LogP 4.26 TPSA 74.6	✓ Ro5	✓ Clean	`CCCCC[C@H](O)C(=O)C/C=C\CCCCCCCC(=O)O`
ZINC14494508	0.657	296.5 Da LogP 4.86 TPSA 57.5	✓ Ro5	✓ Clean	`CCCCC/C=C\C/C=C\[C@@H](O)CCCCCCC(=O)O`
ZINC14494511	0.657	296.5 Da LogP 4.86 TPSA 57.5	✓ Ro5	✓ Clean	`CCCCC/C=C\C/C=C\[C@H](O)CCCCCCC(=O)O`
ZINC138457918	0.654	228.3 Da LogP 3.56 TPSA 54.4	✓ Ro5	✓ Clean	`CCCCCCCC(=O)CCCCC(=O)O`
ZINC138458029	0.654	228.3 Da LogP 3.56 TPSA 54.4	✓ Ro5	✓ Clean	`CCCCCCC(=O)CCCCCC(=O)O`
ZINC196749828	0.654	214.3 Da LogP 3.17 TPSA 54.4	✓ Ro5	✓ Clean	`CCCCCCC(=O)CCCCC(=O)O`
ZINC2113934082	0.654	256.4 Da LogP 4.34 TPSA 54.4	✓ Ro5	✓ Clean	`CCCCCCCC(=O)CCCCCCC(=O)O`
ZINC2113934083	0.654	256.4 Da LogP 4.34 TPSA 54.4	✓ Ro5	✓ Clean	`CCCCCCCCCC(=O)CCCCC(=O)O`
ZINC2243670	0.654	228.3 Da LogP 3.56 TPSA 54.4	✓ Ro5	✓ Clean	`CCCCCC(=O)CCCCCCC(=O)O`
ZINC2569203	0.654	214.3 Da LogP 3.17 TPSA 54.4	✓ Ro5	✓ Clean	`CCCCCC(=O)CCCCCC(=O)O`
ZINC5973005	0.654	242.4 Da LogP 3.95 TPSA 54.4	✓ Ro5	✓ Clean	`CCCCCCC(=O)CCCCCCC(=O)O`
ZINC79244776	0.654	270.4 Da LogP 4.73 TPSA 54.4	✓ Ro5	✓ Clean	`CCCCCCCC(=O)CCCCCCCC(=O)O`
ZINC86037082	0.654	270.4 Da LogP 4.73 TPSA 54.4	✓ Ro5	✓ Clean	`CCCCCCCCCC(=O)CCCCCC(=O)O`
ZINC86039283	0.654	242.4 Da LogP 3.95 TPSA 54.4	✓ Ro5	✓ Clean	`CCCCCCCCC(=O)CCCCC(=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.