Protein profile

KP13_03141

Uridine kinase

Genome: KpKP13

Gene: AHE43644.1 udk Structure source: AlphaFold + ColabFold UniProt A0A0H3GVV7

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Amino acids 213

Annotations 9

Features 25

PDB binders 12

Druggability 0.556

Overview

Basic information about this protein and its source genome.

Accession: KP13_03141
Assembly: Klebsiella pneumoniae subsp. pneumoniae Kp13, complete sequence
Gene: AHE43644.1 udk
Status: annotated
Amino acids: 213
Structure source: AlphaFold + ColabFold

2.7.1.48

GO:0016773 Catalysis of the transfer of a phosphorus-containing group from one compound (donor) to an alcohol group (acceptor). GO:0004849 Catalysis of the reaction: ATP + uridine = ADP + UMP. GO:0016301 Catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule. GO:0005524 Binding to ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator. GO:0005737 The contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures. GO:0043771 Catalysis of the reaction: ATP + cytidine = ADP + CMP.

Target profile

Computed evidence for target prioritization.

Human off-target: hit
Human identity (%): 37.624
Human E-value: 2.91e-42
Gut microbiome off-target: hit
Essential (DEG): Y
DEG identity (%): 68.159
DEG E-value: 6.6999999999999994e-105
Localization: Cytoplasmic
ColabFold pLDDT: 95.52

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 0.556

Structure A0A0H3GVV7

Pocket Pocket 1

P2Rank 0.874

Structure A0A0H3GVV7

Pocket Pocket 1

ColabFold model

FPocket 0.696 · Pocket 1

P2Rank 0.872 · Pocket 1

Core conservation Conserved core gene

Roary core

CoreCruncher core

Gut microbiome 370 / 4744 genomes with a hit

Normalized 0.078

Sequence

Primary amino-acid sequence viewer.

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 8 GO

Enzyme Commission (EC)

2.7.1.48

Gene Ontology (GO)

GO:0016773 Catalysis of the transfer of a phosphorus-containing group from one compound (donor) to an alcohol group (acceptor).
GO:0004849 Catalysis of the reaction: ATP + uridine = ADP + UMP.
GO:0016301 Catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule.
GO:0005524 Binding to ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
GO:0005737 The contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
GO:0043771 Catalysis of the reaction: ATP + cytidine = ADP + CMP.
GO:0044211 Any process which produces cytidine 5'-triphosphate (CTP) from derivatives of it, without de novo synthesis.
GO:0044206 Any process which produces UMP, uridine monophosphate, from derivatives of it (e.g. cytidine, uridine, cytosine) without de novo synthesis.

Sequence Features

Domain/signature hits from InterPro and related databases.

25 records

Show feature table

Start	End	DB	Term	Name
10	208	CDD	cd02023	UMPK
10	208	InterPro	IPR000764	Uridine kinase-like
21	213	Phobius	NON_CYTOPLASMIC_DOMAIN	Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
16	20	Phobius	SIGNAL_PEPTIDE_C_REGION	C-terminal region of a signal peptide.
1	20	Phobius	SIGNAL_PEPTIDE	Signal peptide region
5	213	Hamap	MF_00551	Uridine kinase [udk].
5	213	InterPro	IPR026008	Uridine kinase
1	7	Phobius	SIGNAL_PEPTIDE_N_REGION	N-terminal region of a signal peptide.
5	213	Gene3D	G3DSA:3.40.50.300	-
5	213	InterPro	IPR027417	P-loop containing nucleoside triphosphate hydrolase
7	213	FunFam	G3DSA:3.40.50.300:FF:000252	Uridine kinase
10	199	Pfam	PF00485	Phosphoribulokinase / Uridine kinase family
10	199	InterPro	IPR006083	Phosphoribulokinase/uridine kinase
8	205	SUPERFAMILY	SSF52540	P-loop containing nucleoside triphosphate hydrolases
8	205	InterPro	IPR027417	P-loop containing nucleoside triphosphate hydrolase
8	15	Phobius	SIGNAL_PEPTIDE_H_REGION	Hydrophobic region of a signal peptide.
6	213	NCBIfam	TIGR00235	uridine kinase
6	213	InterPro	IPR000764	Uridine kinase-like
9	190	PANTHER	PTHR10285	URIDINE KINASE
157	168	PRINTS	PR00988	Uridine kinase signature
8	25	PRINTS	PR00988	Uridine kinase signature
87	102	PRINTS	PR00988	Uridine kinase signature
143	153	PRINTS	PR00988	Uridine kinase signature
179	192	PRINTS	PR00988	Uridine kinase signature
42	53	PRINTS	PR00988	Uridine kinase signature

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_A0A0H3GVV7	AlphaFold	—	—	full sequence	—	Viewing
ColabFold KP13_03141	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				0.556
3				0.484
6				0.455

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				16.6	0.782
2				1.04	0.006

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				0.696
5				0.257
3				0.255

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				16.46	0.779
2				0.8	0.003

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.

64 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
0JR	4GI7	B5XYG3	309.4 Da LogP -0.42 TPSA 111.6	✓ Ro5	✓ Clean	`CC(C)(CO)[C@H](C(=O)NCCC(=O)NCc1cccnc1)O`
ACP	3W34	Q5SKR5	505.2 Da LogP -1.52 TPSA 269.9	3 viol.	✓ Clean	`c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)…`
CTN	3W34	Q5SKR5	243.2 Da LogP -2.56 TPSA 130.8	✓ Ro5	✓ Clean	`C1=CN(C(=O)N=C1N)[C@H]2[C@@H]([C@@H]([C@H](O2)C…`
DTT	6KEV	Q31PL2	154.3 Da LogP -0.43 TPSA 40.5	✓ Ro5	✓ Clean	`C([C@@H]([C@H](CS)O)O)S`
G6P	6KEV	Q31PL2	260.1 Da LogP -3.10 TPSA 156.9	1 viol.	✓ Clean	`C([C@@H]1[C@H]([C@@H]([C@H]([C@H](O1)O)O)O)O)OP…`
KEA	6N54	Q9BZX2	348.2 Da LogP -1.13 TPSA 205.9	✓ Ro5	Alert	`C1=CN(C(=O)N=C1N)[C@H]2[C@@H]([C@@H]([C@H](O2)C…`
OS	6HZL	A0A0H3K6J7	190.2 Da LogP -0.00 TPSA 0.0	✓ Ro5	✓ Clean	`[Os+3]`
P6D	6PWZ	Q9BZX2	—	—	—	`C1=CN(C(=O)N=C1N)[C@H]2[C@@H]([C@@H]([C@H](O2)C…`
PN4	4F7W	B5XYG3	288.4 Da LogP 0.18 TPSA 98.7	✓ Ro5	✓ Clean	`CCCCCNC(=O)CCNC(=O)[C@@H](C(C)(C)CO)O`
SH2	4NE2	B5XYG3	366.4 Da LogP -0.04 TPSA 117.1	✓ Ro5	✓ Clean	`CC(C)(CO)[C@H](C(=O)NCCC(=O)NCCc1ccc2c(c1)OCO2)O`
UZ0	6N55	Q9BZX2	269.2 Da LogP -1.53 TPSA 153.3	✓ Ro5	Alert	`C1=CN(C(=O)NC1=O)[C@H]2[C@@H]([C@@H]([C@H](O2)C…`
UZR	6N53	Q9BZX2	350.2 Da LogP -2.18 TPSA 201.4	✓ Ro5	Alert	`C1=CN(C(=O)NC1=O)[C@H]2[C@@H]([C@@H]([C@H](O2)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).

Ligand	UniProt (homolog)	pchembl	MW · LogP · TPSA	Lipinski	PAINS	SMILES
CHEMBL1592234	Q9BZX2	6.00	497.6 Da LogP 5.89 TPSA 101.4	1 viol.	✓ Clean	`Cc1ccc(-c2nc3c(c(SCC(=O)Nc4cccc(C(=O)O)c4)n2)Cc…`
CHEMBL4787313	Q9BZX2	—	715.3 Da LogP 0.35 TPSA 129.5	1 viol.	✓ Clean	`COc1c(OCCOCCOCCNC(=O)CCCC[C@@H]2SC[C@@H]3NC(=O)…`

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
ZINC1078621	1.000	243.2 Da LogP -2.56 TPSA 130.8	✓ Ro5	✓ Clean	`Nc1ccn([C@H]2O[C@H](CO)[C@@H](O)[C@H]2O)c(=O)n1`
ZINC12336757	1.000	243.2 Da LogP -2.56 TPSA 130.8	✓ Ro5	✓ Clean	`Nc1ccn([C@@H]2O[C@H](CO)[C@H](O)[C@@H]2O)c(=O)n1`
ZINC12336758	1.000	243.2 Da LogP -2.56 TPSA 130.8	✓ Ro5	✓ Clean	`Nc1ccn([C@H]2O[C@H](CO)[C@H](O)[C@@H]2O)c(=O)n1`
ZINC146563393	1.000	269.2 Da LogP -1.53 TPSA 153.3	✓ Ro5	Alert	`[N-]=[N+]=N[C@H]1[C@@H](O)[C@@H](CO)O[C@H]1n1cc…`
ZINC16969357	1.000	243.2 Da LogP -2.56 TPSA 130.8	✓ Ro5	✓ Clean	`Nc1ccn([C@H]2O[C@@H](CO)[C@H](O)[C@H]2O)c(=O)n1`
ZINC17261182	1.000	269.2 Da LogP -1.53 TPSA 153.3	✓ Ro5	Alert	`[N-]=[N+]=N[C@H]1[C@H](O)[C@@H](CO)O[C@@H]1n1cc…`
ZINC230402123	1.000	269.2 Da LogP -1.53 TPSA 153.3	✓ Ro5	Alert	`[N-]=[N+]=N[C@H]1[C@@H](n2ccc(=O)[nH]c2=O)O[C@H…`
ZINC230402126	1.000	269.2 Da LogP -1.53 TPSA 153.3	✓ Ro5	Alert	`[N-]=[N+]=N[C@@H]1[C@@H](n2ccc(=O)[nH]c2=O)O[C@…`
ZINC230402130	1.000	269.2 Da LogP -1.53 TPSA 153.3	✓ Ro5	Alert	`[N-]=[N+]=N[C@@H]1[C@H](O)[C@@H](CO)O[C@@H]1n1c…`
ZINC2583632	1.000	243.2 Da LogP -2.56 TPSA 130.8	✓ Ro5	✓ Clean	`Nc1ccn([C@@H]2O[C@H](CO)[C@@H](O)[C@H]2O)c(=O)n1`
ZINC3795098	1.000	243.2 Da LogP -2.56 TPSA 130.8	✓ Ro5	✓ Clean	`Nc1ccn([C@@H]2O[C@H](CO)[C@@H](O)[C@@H]2O)c(=O)…`
ZINC3830623	1.000	243.2 Da LogP -2.56 TPSA 130.8	✓ Ro5	✓ Clean	`Nc1ccn([C@H]2O[C@@H](CO)[C@@H](O)[C@H]2O)c(=O)n1`
ZINC3830624	1.000	243.2 Da LogP -2.56 TPSA 130.8	✓ Ro5	✓ Clean	`Nc1ccn([C@@H]2O[C@@H](CO)[C@@H](O)[C@H]2O)c(=O)…`
ZINC3978018	1.000	243.2 Da LogP -2.56 TPSA 130.8	✓ Ro5	✓ Clean	`Nc1ccn([C@H]2O[C@H](CO)[C@@H](O)[C@@H]2O)c(=O)n1`
ZINC4521169	1.000	269.2 Da LogP -1.53 TPSA 153.3	✓ Ro5	Alert	`[N-]=[N+]=N[C@@H]1[C@H](O)[C@H](CO)O[C@@H]1n1cc…`
ZINC4521170	1.000	269.2 Da LogP -1.53 TPSA 153.3	✓ Ro5	Alert	`[N-]=[N+]=N[C@@H]1[C@H](O)[C@H](CO)O[C@H]1n1ccc…`
ZINC4521171	1.000	269.2 Da LogP -1.53 TPSA 153.3	✓ Ro5	Alert	`[N-]=[N+]=N[C@H]1[C@H](O)[C@H](CO)O[C@@H]1n1ccc…`
ZINC4521172	1.000	269.2 Da LogP -1.53 TPSA 153.3	✓ Ro5	Alert	`[N-]=[N+]=N[C@H]1[C@H](O)[C@H](CO)O[C@H]1n1ccc(…`
ZINC6091560	1.000	269.2 Da LogP -1.53 TPSA 153.3	✓ Ro5	Alert	`[N-]=[N+]=N[C@@H]1[C@H](O)[C@@H](CO)O[C@H]1n1cc…`
ZINC6091575	1.000	243.2 Da LogP -2.56 TPSA 130.8	✓ Ro5	✓ Clean	`Nc1ccn([C@@H]2O[C@H](CO)[C@H](O)[C@H]2O)c(=O)n1`
ZINC6234828	1.000	243.2 Da LogP -2.56 TPSA 130.8	✓ Ro5	✓ Clean	`Nc1ccn([C@H]2O[C@H](CO)[C@H](O)[C@H]2O)c(=O)n1`
ZINC6524892	1.000	243.2 Da LogP -2.56 TPSA 130.8	✓ Ro5	✓ Clean	`Nc1ccn([C@@H]2O[C@@H](CO)[C@H](O)[C@H]2O)c(=O)n1`
ZINC83301154	1.000	269.2 Da LogP -1.53 TPSA 153.3	✓ Ro5	Alert	`[N-]=[N+]=N[C@@H]1[C@@H](n2ccc(=O)[nH]c2=O)O[C@…`
ZINC895248	1.000	243.2 Da LogP -2.56 TPSA 130.8	✓ Ro5	✓ Clean	`Nc1ccn([C@H]2O[C@@H](CO)[C@H](O)[C@@H]2O)c(=O)n1`
ZINC90697708	1.000	269.2 Da LogP -1.53 TPSA 153.3	✓ Ro5	Alert	`[N-]=[N+]=N[C@@H]1[C@@H](O)[C@@H](CO)O[C@H]1n1c…`
ZINC34268101	0.848	269.2 Da LogP -1.53 TPSA 153.3	✓ Ro5	Alert	`[N-]=[N+]=N[C@@H]1[C@H](CO)O[C@H](n2ccc(=O)[nH]…`
ZINC34268103	0.848	269.2 Da LogP -1.53 TPSA 153.3	✓ Ro5	Alert	`[N-]=[N+]=N[C@H]1[C@H](O)[C@@H](n2ccc(=O)[nH]c2…`
ZINC12360002	0.839	427.2 Da LogP -1.75 TPSA 232.6	2 viol.	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@H](CO[P@@](=O)(O)OP(=O…`
ZINC12360703	0.839	427.2 Da LogP -1.75 TPSA 232.6	2 viol.	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@H](CO[P@@](=O)(O)OP(=O…`
ZINC12503599	0.839	427.2 Da LogP -1.75 TPSA 232.6	2 viol.	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@H](CO[P@@](=O)(O)OP(=O…`
ZINC16546165	0.839	427.2 Da LogP -1.75 TPSA 232.6	2 viol.	✓ Clean	`Nc1ncnc2c1ncn2[C@H]1O[C@H](CO[P@](=O)(O)OP(=O)(…`
ZINC31977053	0.839	427.2 Da LogP -1.75 TPSA 232.6	2 viol.	✓ Clean	`Nc1ncnc2c1ncn2[C@H]1O[C@@H](CO[P@](=O)(O)OP(=O)…`
ZINC4806433	0.839	427.2 Da LogP -1.75 TPSA 232.6	2 viol.	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@H](CO[P@@](=O)(O)OP(=O…`
ZINC53683898	0.839	427.2 Da LogP -1.75 TPSA 232.6	2 viol.	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@@H](CO[P@@](=O)(O)OP(=…`
ZINC8586019	0.839	427.2 Da LogP -1.75 TPSA 232.6	2 viol.	✓ Clean	`Nc1ncnc2c1ncn2[C@H]1O[C@@H](CO[P@](=O)(O)OP(=O)…`
ZINC8586020	0.839	427.2 Da LogP -1.75 TPSA 232.6	2 viol.	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@@H](CO[P@@](=O)(O)OP(=…`
ZINC8586021	0.839	427.2 Da LogP -1.75 TPSA 232.6	2 viol.	✓ Clean	`Nc1ncnc2c1ncn2[C@H]1O[C@@H](CO[P@@](=O)(O)OP(=O…`
ZINC8586022	0.839	427.2 Da LogP -1.75 TPSA 232.6	2 viol.	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@@H](CO[P@@](=O)(O)OP(=…`
ZINC34085615	0.829	242.2 Da LogP -2.60 TPSA 136.6	✓ Ro5	✓ Clean	`Nc1ccn([C@@H]2O[C@H](CO)[C@@H](O)[C@H]2N)c(=O)n1`
ZINC13546396	0.810	245.2 Da LogP -1.59 TPSA 110.6	✓ Ro5	✓ Clean	`Nc1ccn([C@@H]2O[C@H](CO)[C@H](O)[C@H]2F)c(=O)n1`
ZINC16952044	0.810	245.2 Da LogP -1.59 TPSA 110.6	✓ Ro5	✓ Clean	`Nc1ccn([C@H]2O[C@@H](CO)[C@H](O)[C@H]2F)c(=O)n1`
ZINC17174505	0.810	245.2 Da LogP -1.59 TPSA 110.6	✓ Ro5	✓ Clean	`Nc1ccn([C@@H]2O[C@@H](CO)[C@@H](O)[C@@H]2F)c(=O…`
ZINC17174506	0.810	245.2 Da LogP -1.59 TPSA 110.6	✓ Ro5	✓ Clean	`Nc1ccn([C@@H]2O[C@H](CO)[C@@H](O)[C@@H]2F)c(=O)…`
ZINC2522524	0.810	245.2 Da LogP -1.59 TPSA 110.6	✓ Ro5	✓ Clean	`Nc1ccn([C@H]2O[C@@H](CO)[C@H](O)[C@@H]2F)c(=O)n1`
ZINC3817231	0.810	245.2 Da LogP -1.59 TPSA 110.6	✓ Ro5	✓ Clean	`Nc1ccn([C@@H]2O[C@H](CO)[C@@H](O)[C@H]2F)c(=O)n1`
ZINC57331	0.810	245.2 Da LogP -1.59 TPSA 110.6	✓ Ro5	✓ Clean	`Nc1ccn([C@@H]2O[C@@H](CO)[C@@H](O)[C@H]2F)c(=O)…`
ZINC5758597	0.810	245.2 Da LogP -1.59 TPSA 110.6	✓ Ro5	✓ Clean	`Nc1ccn([C@H]2O[C@@H](CO)[C@@H](O)[C@H]2F)c(=O)n1`
ZINC5758598	0.810	245.2 Da LogP -1.59 TPSA 110.6	✓ Ro5	✓ Clean	`Nc1ccn([C@H]2O[C@@H](CO)[C@@H](O)[C@@H]2F)c(=O)…`
ZINC59201305	0.810	245.2 Da LogP -1.59 TPSA 110.6	✓ Ro5	✓ Clean	`Nc1ccn([C@@H]2O[C@H](CO)[C@H](O)[C@@H]2F)c(=O)n1`
ZINC85475812	0.786	245.2 Da LogP -1.59 TPSA 110.6	✓ Ro5	✓ Clean	`Nc1ccn([C@@H]2O[C@H](CO)[C@H](F)[C@H]2O)c(=O)n1`

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.