Protein profile

KP13_04326

HTH-type transcriptional regulator perR

Genome: KpKP13

Gene: perR AHE45560.1 Structure source: AlphaFold + ColabFold UniProt A0A0H3GQJ5

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Amino acids 307

Annotations 4

Features 21

PDB binders 3

Druggability 0.499

Overview

Basic information about this protein and its source genome.

Accession: KP13_04326
Assembly: Klebsiella pneumoniae subsp. pneumoniae Kp13, complete sequence
Gene: perR AHE45560.1
Status: annotated
Amino acids: 307
Structure source: AlphaFold + ColabFold

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. 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:0006351 The synthesis of an RNA transcript from a DNA template.

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: 90.08

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 0.499

Structure A0A0H3GQJ5

Pocket Pocket 18

P2Rank 0.322

Structure A0A0H3GQJ5

Pocket Pocket 1

ColabFold model

FPocket 0.422 · Pocket 16

P2Rank 0.301 · Pocket 1

Core conservation Conserved core gene

Roary core

CoreCruncher core

Gut microbiome 15 / 4744 genomes with a hit

Normalized 0.003

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: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: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:0006351 The synthesis of an RNA transcript from a DNA template.

Sequence Features

Domain/signature hits from InterPro and related databases.

21 records

Show feature table

Start	End	DB	Term	Name
171	270	Gene3D	G3DSA:3.40.190.10	-
103	299	Pfam	PF03466	LysR substrate binding domain
103	299	InterPro	IPR005119	LysR, substrate-binding
41	51	PRINTS	PR00039	LysR bacterial regulatory protein HTH signature
41	51	InterPro	IPR000847	Transcription regulator HTH, LysR
30	41	PRINTS	PR00039	LysR bacterial regulatory protein HTH signature
30	41	InterPro	IPR000847	Transcription regulator HTH, LysR
51	62	PRINTS	PR00039	LysR bacterial regulatory protein HTH signature
51	62	InterPro	IPR000847	Transcription regulator HTH, LysR
15	74	Pfam	PF00126	Bacterial regulatory helix-turn-helix protein, lysR family
15	74	InterPro	IPR000847	Transcription regulator HTH, LysR
106	295	Gene3D	G3DSA:3.40.190.10	-
102	303	SUPERFAMILY	SSF53850	Periplasmic binding protein-like II
13	70	ProSiteProfiles	PS50931	LysR-type HTH domain profile.
13	70	InterPro	IPR000847	Transcription regulator HTH, LysR
15	301	PANTHER	PTHR30537	HTH-TYPE TRANSCRIPTIONAL REGULATOR
12	96	FunFam	G3DSA:1.10.10.10:FF:000001	LysR family transcriptional regulator
7	95	Gene3D	G3DSA:1.10.10.10	-
7	95	InterPro	IPR036388	Winged helix-like DNA-binding domain superfamily
8	121	SUPERFAMILY	SSF46785	Winged helix DNA-binding domain
8	121	InterPro	IPR036390	Winged helix 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_A0A0H3GQJ5	AlphaFold	—	—	full sequence	—	Viewing
ColabFold KP13_04326	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
7				0.14
22				0.126
3				0.001
4				0.001

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	7.33	0.322
2	2.54	0.058
3	1.47	0.017
4	1.45	0.016

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
16				0.422

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	2.77	0.085
2	2.07	0.046
3	1.91	0.039
4	1.24	0.012

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
6DB	5VVI	P0A4T4	246.3 Da LogP -1.23 TPSA 148.5	1 viol.	✓ Clean	`[H]/N=C(/N)\NCCC[C@@H](C(=O)O)N[C@H](C)C(=O)O`
CCU	3GLB	P07774	142.1 Da LogP 0.27 TPSA 74.6	✓ Ro5	✓ Clean	`C(=C/C(=O)O)/C=C\C(=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
ZINC34564963	0.900	248.3 Da LogP 2.91 TPSA 54.4	✓ Ro5	✓ Clean	`Cc1ccc(-c2ccc(S(=O)(=O)O)cc2)cc1`
ZINC1529866	0.833	246.3 Da LogP -1.23 TPSA 148.5	1 viol.	✓ Clean	`C[C@H](N[C@@H](CCCNC(=N)N)C(=O)O)C(=O)O`
ZINC1529867	0.833	246.3 Da LogP -1.23 TPSA 148.5	1 viol.	✓ Clean	`C[C@@H](N[C@@H](CCCNC(=N)N)C(=O)O)C(=O)O`
ZINC6093151	0.722	238.2 Da LogP 0.18 TPSA 108.7	✓ Ro5	✓ Clean	`O=S(=O)(O)c1ccc(S(=O)(=O)O)cc1`
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`
ZINC82548310	0.636	236.3 Da LogP 0.34 TPSA 88.5	✓ Ro5	✓ Clean	`CS(=O)(=O)c1ccc(S(=O)(=O)O)cc1`
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`
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`
ZINC1669673	0.577	206.7 Da LogP 1.90 TPSA 54.4	✓ Ro5	✓ Clean	`Cc1ccc(S(=O)(=O)O)cc1Cl`
ZINC1529261	0.571	304.3 Da LogP -1.39 TPSA 185.8	1 viol.	✓ Clean	`N=C(N)NCCC[C@@H](N[C@@H](CCC(=O)O)C(=O)O)C(=O)O`
ZINC1529262	0.571	304.3 Da LogP -1.39 TPSA 185.8	1 viol.	✓ Clean	`N=C(N)NCCC[C@@H](N[C@H](CCC(=O)O)C(=O)O)C(=O)O`
ZINC1529939	0.571	304.3 Da LogP -1.39 TPSA 185.8	1 viol.	✓ Clean	`N=C(N)NCCC[C@H](N[C@@H](CCC(=O)O)C(=O)O)C(=O)O`
ZINC1529940	0.571	304.3 Da LogP -1.39 TPSA 185.8	1 viol.	✓ Clean	`N=C(N)NCCC[C@H](N[C@H](CCC(=O)O)C(=O)O)C(=O)O`
ZINC1729188	0.565	237.1 Da LogP 1.70 TPSA 54.4	✓ Ro5	✓ Clean	`O=S(=O)(O)c1ccc(Br)cc1`
ZINC2166861	0.565	326.4 Da LogP 2.40 TPSA 77.5	✓ Ro5	✓ Clean	`Cc1ccc(S(=O)(=O)OS(=O)(=O)c2ccc(C)cc2)cc1`
ZINC3619328	0.565	284.1 Da LogP 1.54 TPSA 54.4	✓ Ro5	✓ Clean	`O=S(=O)(O)c1ccc(I)cc1`
ZINC2522560	0.564	204.2 Da LogP -0.76 TPSA 112.6	✓ Ro5	✓ Clean	`C[C@@H](N[C@@H](CCCN)C(=O)O)C(=O)O`
ZINC1593169	0.560	248.3 Da LogP 2.53 TPSA 54.4	✓ Ro5	✓ Clean	`Cc1ccc(S(=O)(=O)c2ccc(O)cc2)cc1`
ZINC1666834	0.560	201.2 Da LogP 1.00 TPSA 57.6	✓ Ro5	✓ Clean	`CN(C)c1ccc(S(=O)(=O)O)cc1`
ZINC1669748	0.560	249.3 Da LogP 2.18 TPSA 80.4	✓ Ro5	✓ Clean	`Nc1ccc(-c2ccc(S(=O)(=O)O)cc2)cc1`
ZINC16954679	0.560	405.3 Da LogP 4.16 TPSA 68.3	✓ Ro5	✓ Clean	`Cc1ccc(S(=O)(=O)/C(Cl)=C(\Cl)S(=O)(=O)c2ccc(C)c…`
ZINC1725634	0.560	405.3 Da LogP 4.16 TPSA 68.3	✓ Ro5	✓ Clean	`Cc1ccc(S(=O)(=O)/C(Cl)=C(/Cl)S(=O)(=O)c2ccc(C)c…`
ZINC2018553	0.560	200.3 Da LogP 2.06 TPSA 54.4	✓ Ro5	✓ Clean	`CC(C)c1ccc(S(=O)(=O)O)cc1`
ZINC2166812	0.560	200.2 Da LogP 1.14 TPSA 71.4	✓ Ro5	✓ Clean	`CC(=O)c1ccc(S(=O)(=O)O)cc1`
ZINC285824	0.560	336.4 Da LogP 3.02 TPSA 68.3	✓ Ro5	✓ Clean	`C=C(S(=O)(=O)c1ccc(C)cc1)S(=O)(=O)c1ccc(C)cc1`
ZINC34553177	0.560	268.7 Da LogP 3.25 TPSA 54.4	✓ Ro5	✓ Clean	`O=S(=O)(O)c1ccc(-c2ccc(Cl)cc2)cc1`
ZINC35569526	0.560	252.3 Da LogP 2.74 TPSA 54.4	✓ Ro5	✓ Clean	`O=S(=O)(O)c1ccc(-c2ccc(F)cc2)cc1`
ZINC453223	0.560	224.2 Da LogP 2.29 TPSA 34.1	✓ Ro5	✓ Clean	`Cc1ccc(S(=O)(=O)C(F)(F)F)cc1`
ZINC1593172	0.556	276.3 Da LogP 2.53 TPSA 71.4	✓ Ro5	✓ Clean	`Cc1ccc(S(=O)(=O)c2ccc(C(=O)O)cc2)cc1`
ZINC1644074	0.556	251.1 Da LogP 2.00 TPSA 54.4	✓ Ro5	✓ Clean	`Cc1cc(S(=O)(=O)O)ccc1Br`
ZINC1680427	0.556	206.7 Da LogP 1.90 TPSA 54.4	✓ Ro5	✓ Clean	`Cc1cc(S(=O)(=O)O)ccc1Cl`
ZINC35569528	0.556	264.3 Da LogP 2.61 TPSA 63.6	✓ Ro5	✓ Clean	`COc1ccc(-c2ccc(S(=O)(=O)O)cc2)cc1`
ZINC1529832	0.550	218.3 Da LogP -0.37 TPSA 112.6	✓ Ro5	✓ Clean	`C[C@@H](N[C@@H](CCCCN)C(=O)O)C(=O)O`
ZINC2168595	0.548	313.4 Da LogP 4.14 TPSA 66.4	✓ Ro5	✓ Clean	`Cc1ccc(Nc2ccc3cc(S(=O)(=O)O)ccc3c2)cc1`
ZINC1847640	0.548	216.2 Da LogP -1.16 TPSA 128.3	✓ Ro5	✓ Clean	`CC(=O)N[C@@H](CCCNC(=N)N)C(=O)O`
ZINC2169795	0.548	216.2 Da LogP -1.16 TPSA 128.3	✓ Ro5	✓ Clean	`CC(=O)N[C@H](CCCNC(=N)N)C(=O)O`
ZINC2579085	0.545	245.3 Da LogP -1.83 TPSA 154.3	1 viol.	✓ Clean	`C[C@H](N)C(=O)N[C@@H](CCCNC(=N)N)C(=O)O`
ZINC8577164	0.545	245.3 Da LogP -1.83 TPSA 154.3	1 viol.	✓ Clean	`C[C@@H](N)C(=O)N[C@@H](CCCNC(=N)N)C(=O)O`
ZINC100567765	0.542	336.4 Da LogP 3.02 TPSA 68.3	✓ Ro5	✓ Clean	`Cc1ccc(S(=O)(=O)/C=C\S(=O)(=O)c2ccc(C)cc2)cc1`
ZINC1561847	0.542	346.4 Da LogP 2.33 TPSA 108.7	✓ Ro5	✓ Clean	`O=S(=O)(O)c1ccc(Sc2ccc(S(=O)(=O)O)cc2)cc1`
ZINC1670114	0.542	344.4 Da LogP 1.62 TPSA 132.8	✓ Ro5	✓ Clean	`O=S(=O)(O)c1ccc(NNc2ccc(S(=O)(=O)O)cc2)cc1`
ZINC1712055	0.542	324.4 Da LogP 2.51 TPSA 68.3	✓ Ro5	✓ Clean	`Cc1ccc(S(=O)(=O)CS(=O)(=O)c2ccc(C)cc2)cc1`
ZINC1725610	0.542	336.4 Da LogP 3.02 TPSA 68.3	✓ Ro5	✓ Clean	`Cc1ccc(S(=O)(=O)/C=C/S(=O)(=O)c2ccc(C)cc2)cc1`
ZINC1730097	0.542	340.4 Da LogP 1.48 TPSA 92.3	✓ Ro5	✓ Clean	`Cc1ccc(S(=O)(=O)NNS(=O)(=O)c2ccc(C)cc2)cc1`
ZINC34089747	0.542	330.3 Da LogP 1.97 TPSA 118.0	✓ Ro5	✓ Clean	`O=S(=O)(O)c1ccc(Oc2ccc(S(=O)(=O)O)cc2)cc1`
ZINC3845142	0.542	342.4 Da LogP 2.60 TPSA 133.5	✓ Ro5	Alert	`O=S(=O)(O)c1ccc(/N=N/c2ccc(S(=O)(=O)O)cc2)cc1`
ZINC397599	0.542	325.4 Da LogP 1.97 TPSA 80.3	✓ Ro5	✓ Clean	`Cc1ccc(S(=O)(=O)NS(=O)(=O)c2ccc(C)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.