Target Pathogen

Overview

Basic information about this protein and its source genome.

Accession: KP13_03935
Assembly: Klebsiella pneumoniae subsp. pneumoniae Kp13, complete sequence
Gene: uidR AHE45320.1
Status: annotated
Amino acids: 190
Structure source: AlphaFold + ColabFold

GO

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:0000976 Binding to a specific sequence of DNA that is part of a regulatory region that controls transcription of that section of the DNA. The transcribed region might be described as a gene, cistron, or operon.

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: 94.91

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 0.711

Structure A0A422YMN3

Pocket Pocket 1

P2Rank 0.923

Structure A0A422YMN3

Pocket Pocket 1

ColabFold model

FPocket 0.861 · Pocket 1

P2Rank 0.75 · Pocket 1

Core conservation Accessory gene

Roary accessory

CoreCruncher accessory

Gut microbiome 7 / 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)

3

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:0000976 Binding to a specific sequence of DNA that is part of a regulatory region that controls transcription of that section of the DNA. The transcribed region might be described as a gene, cistron, or operon.

Sequence Features

Domain/signature hits from InterPro and related databases.

24 records

Show feature table

Start	End	DB	Term	Name
1	25	Phobius	SIGNAL_PEPTIDE	Signal peptide region
23	54	ProSitePatterns	PS01081	TetR-type HTH domain signature.
23	54	InterPro	IPR023772	DNA-binding HTH domain, TetR-type, conserved site
5	65	ProSiteProfiles	PS50977	TetR-type HTH domain profile.
5	65	InterPro	IPR001647	DNA-binding HTH domain, TetR-type
21	25	Phobius	SIGNAL_PEPTIDE_C_REGION	C-terminal region of a signal peptide.
11	20	Phobius	SIGNAL_PEPTIDE_H_REGION	Hydrophobic region of a signal peptide.
52	190	Gene3D	G3DSA:1.10.357.10	Tetracycline Repressor, domain 2
99	169	Pfam	PF13977	BetI-type transcriptional repressor, C-terminal
99	169	InterPro	IPR039538	BetI-type transcriptional repressor, C-terminal
1	10	Phobius	SIGNAL_PEPTIDE_N_REGION	N-terminal region of a signal peptide.
2	51	Gene3D	G3DSA:1.10.10.60	-
11	57	Pfam	PF00440	Bacterial regulatory proteins, tetR family
11	57	InterPro	IPR001647	DNA-binding HTH domain, TetR-type
76	186	SUPERFAMILY	SSF48498	Tetracyclin repressor-like, C-terminal domain
76	186	InterPro	IPR036271	Tetracyclin repressor-like, C-terminal domain superfamily
26	190	Phobius	NON_CYTOPLASMIC_DOMAIN	Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
9	166	PANTHER	PTHR30055	HTH-TYPE TRANSCRIPTIONAL REGULATOR RUTR
11	24	PRINTS	PR00455	TetR bacterial regulatory protein HTH signature
11	24	InterPro	IPR001647	DNA-binding HTH domain, TetR-type
32	55	PRINTS	PR00455	TetR bacterial regulatory protein HTH signature
32	55	InterPro	IPR001647	DNA-binding HTH domain, TetR-type
3	71	SUPERFAMILY	SSF46689	Homeodomain-like
3	71	InterPro	IPR009057	Homeobox-like 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_A0A422YMN3	AlphaFold	—	—	full sequence	—	Viewing
ColabFold KP13_03935	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				0.711

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				24.66	0.9

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				0.861

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				14.56	0.726
2				1.55	0.023

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.

22 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
B3P	4ICH	C7MT25	282.3 Da LogP -4.01 TPSA 145.4	1 viol.	✓ Clean	`C(CNC(CO)(CO)CO)CNC(CO)(CO)CO`
BEN	4JNN	C7MT25	120.2 Da LogP 0.97 TPSA 49.9	✓ Ro5	✓ Clean	`[H]/N=C(\c1ccccc1)/N`
CHT	4KWA	C7MT25	104.2 Da LogP -0.32 TPSA 20.2	✓ Ro5	✓ Clean	`C[N+](C)(C)CCO`
DCC	1VI0	P94548	949.8 Da LogP 2.59 TPSA 363.6	3 viol.	✓ Clean	`CCCCCCCCCCCC(=O)SCCNC(=O)CCNC(=O)[C@@H](C(C)(C)…`
KEN	4NEL	C7MT25	59.1 Da LogP 0.18 TPSA 3.2	✓ Ro5	✓ Clean	`CN(C)C`
ST9	3WHC	P94548	1034.0 Da LogP 4.93 TPSA 363.6	3 viol.	✓ Clean	`CCCCCCCCCCCCCCCCCC(=O)SCCNC(=O)CCNC(=O)[C@@H](C…`

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
ZINC4521259	1.000	282.3 Da LogP -4.01 TPSA 145.4	1 viol.	✓ Clean	`OCC(CO)(CO)NCCCNC(CO)(CO)CO`
ZINC115591405	0.636	373.6 Da LogP 4.55 TPSA 72.7	✓ Ro5	✓ Clean	`CCCCCCCCCCCCCCCCCCNC(CO)(CO)CO`
ZINC115591837	0.636	317.5 Da LogP 2.99 TPSA 72.7	✓ Ro5	✓ Clean	`CCCCCCCCCCCCCCNC(CO)(CO)CO`
ZINC143575268	0.636	289.5 Da LogP 2.21 TPSA 72.7	✓ Ro5	✓ Clean	`CCCCCCCCCCCCNC(CO)(CO)CO`
ZINC2322313	0.636	233.4 Da LogP 0.65 TPSA 72.7	✓ Ro5	✓ Clean	`CCCCCCCCNC(CO)(CO)CO`
ZINC97996983	0.636	345.6 Da LogP 3.77 TPSA 72.7	✓ Ro5	✓ Clean	`CCCCCCCCCCCCCCCCNC(CO)(CO)CO`
ZINC1611594	0.583	243.3 Da LogP -2.43 TPSA 127.1	✓ Ro5	✓ Clean	`O=S(=O)(O)CCCNC(CO)(CO)CO`
ZINC5273895	0.583	257.3 Da LogP -2.04 TPSA 127.1	✓ Ro5	✓ Clean	`O=S(=O)(O)CCCCNC(CO)(CO)CO`
ZINC12501123	0.516	427.2 Da LogP -1.75 TPSA 232.6	2 viol.	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@H](COP(=O)(O)O)[C@@H](…`
ZINC4228234	0.516	427.2 Da LogP -1.75 TPSA 232.6	2 viol.	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@H](COP(=O)(O)O)[C@@H](…`
ZINC79671662	0.516	427.2 Da LogP -1.75 TPSA 232.6	2 viol.	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@H](COP(=O)(O)O)[C@H](O…`
ZINC79671663	0.516	427.2 Da LogP -1.75 TPSA 232.6	2 viol.	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@H](COP(=O)(O)O)[C@H](O…`
ZINC100368719	0.500	210.3 Da LogP 2.43 TPSA 52.0	✓ Ro5	✓ Clean	`N/C(=C(\N)c1ccccc1)c1ccccc1`
ZINC1530141	0.500	229.3 Da LogP -2.82 TPSA 127.1	✓ Ro5	✓ Clean	`O=S(=O)(O)CCNC(CO)(CO)CO`
ZINC24716871	0.500	210.3 Da LogP 2.43 TPSA 52.0	✓ Ro5	✓ Clean	`N/C(=C(/N)c1ccccc1)c1ccccc1`
ZINC5771971	0.500	238.3 Da LogP 1.71 TPSA 76.8	✓ Ro5	✓ Clean	`N/C(=N\N=C(/N)c1ccccc1)c1ccccc1`

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.

KP13_03935

Overview

Target profile

Selected Druggability evidence

Sequence

Functional Annotations

Gene Ontology (GO)

Sequence Features

3D Structure

Structural evidence

Pockets (FPOCKET)

Pockets (P2RANK)

Pockets (FPOCKET)

Pockets (P2RANK)

Ligand evidence