Protein profile

KP13_04700

Thymidine kinase

Genome: KpKP13

Gene: tdk AHE44038.1 Structure source: AlphaFold + ColabFold UniProt W8UYI4

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Amino acids 205

Annotations 7

Features 17

PDB binders 5

Druggability 0.903

Overview

Basic information about this protein and its source genome.

Accession: KP13_04700
Assembly: Klebsiella pneumoniae subsp. pneumoniae Kp13, complete sequence
Gene: tdk AHE44038.1
Status: annotated
Amino acids: 205
Structure source: AlphaFold + ColabFold

2.7.1.21

GO:0005524 Binding to ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator. GO:0004797 Catalysis of the reaction: ATP + thymidine = ADP + thymidine 5'-phosphate. GO:0005829 The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes. GO:0008270 Binding to a zinc ion (Zn). GO:0071897 The biosynthetic process resulting in the formation of DNA. GO:0046104 The chemical reactions and pathways involving thymidine, deoxyribosylthymine thymine 2-deoxyriboside, a deoxynucleoside very widely distributed but occurring almost entirely as phosphoric esters in deoxynucleotides and deoxyribonucleic acid, DNA.

Target profile

Computed evidence for target prioritization.

Human off-target: No hit
Human identity (%): 0.0
Gut microbiome off-target: hit
Essential (DEG): Y
DEG identity (%): 88.67
DEG E-value: 1.82e-135
Localization: Cytoplasmic
ColabFold pLDDT: 93.09

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 0.903

Structure W8UYI4

Pocket Pocket 1

P2Rank 0.547

Structure W8UYI4

Pocket Pocket 1

ColabFold model

FPocket 0.748 · Pocket 1

P2Rank 0.837 · Pocket 1

Core conservation Accessory gene

Roary core

CoreCruncher accessory

Gut microbiome 248 / 4744 genomes with a hit

Normalized 0.052

Sequence

Primary amino-acid sequence viewer.

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 6 GO

Enzyme Commission (EC)

2.7.1.21

Gene Ontology (GO)

GO:0005524 Binding to ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
GO:0004797 Catalysis of the reaction: ATP + thymidine = ADP + thymidine 5'-phosphate.
GO:0005829 The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
GO:0008270 Binding to a zinc ion (Zn).
GO:0071897 The biosynthetic process resulting in the formation of DNA.
GO:0046104 The chemical reactions and pathways involving thymidine, deoxyribosylthymine thymine 2-deoxyriboside, a deoxynucleoside very widely distributed but occurring almost entirely as phosphoric esters in deoxynucleotides and deoxyribonucleic acid, DNA.

Sequence Features

Domain/signature hits from InterPro and related databases.

17 records

Show feature table

Start	End	DB	Term	Name
2	198	PANTHER	PTHR11441	THYMIDINE KINASE
2	198	InterPro	IPR001267	Thymidine kinase
1	141	FunFam	G3DSA:3.40.50.300:FF:000323	Thymidine kinase
142	189	SUPERFAMILY	SSF57716	Glucocorticoid receptor-like (DNA-binding domain)
1	189	Hamap	MF_00124	Thymidine kinase [tdk].
1	189	InterPro	IPR001267	Thymidine kinase
143	187	Gene3D	G3DSA:3.30.60.20	-
1	141	SUPERFAMILY	SSF52540	P-loop containing nucleoside triphosphate hydrolases
1	141	InterPro	IPR027417	P-loop containing nucleoside triphosphate hydrolase
2	186	Pfam	PF00265	Thymidine kinase
2	186	InterPro	IPR001267	Thymidine kinase
1	141	Gene3D	G3DSA:3.40.50.300	-
143	187	FunFam	G3DSA:3.30.60.20:FF:000017	Thymidine kinase
173	186	ProSitePatterns	PS00603	Thymidine kinase cellular-type signature.
173	186	InterPro	IPR020633	Thymidine kinase, conserved site
1	201	PIRSF	PIRSF035805	Tdk
1	201	InterPro	IPR001267	Thymidine kinase

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_W8UYI4	AlphaFold	—	—	full sequence	—	Viewing
ColabFold KP13_04700	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				0.903

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	8.0	0.425
2	6.55	0.331
3	1.02	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				0.748

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				15.73	0.76

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.

58 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
4TA	2ORW	Q9WYN2	807.3 Da LogP -4.51 TPSA 410.3	2 viol.	✓ Clean	`CC1=CN(C(=O)NC1=O)[C@H]2C[C@@H]([C@H](O2)COP(=O…`
ANP	2QQ0	Q9WYN2	506.2 Da LogP -2.06 TPSA 281.9	3 viol.	✓ Clean	`c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)…`
QBT	5FUW	Q38CF2	324.2 Da LogP -1.24 TPSA 145.6	✓ Ro5	✓ Clean	`C[C@H]1CN(C(=O)NC1=O)[C@H]2C[C@@H]([C@H](O2)COP…`
THM	5FUV	Q38CF2	242.2 Da LogP -1.51 TPSA 104.6	✓ Ro5	✓ Clean	`CC1=CN(C(=O)NC1=O)[C@H]2C[C@@H]([C@H](O2)CO)O`
TTP	2J87	O57203	482.2 Da LogP -1.16 TPSA 244.1	2 viol.	✓ Clean	`CC1=CN(C(=O)NC1=O)[C@H]2C[C@@H]([C@H](O2)CO[P@]…`

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
CHEMBL3229680	P09768	—	511.2 Da LogP -1.04 TPSA 256.2	3 viol.	✓ Clean	`CCNc1cn([C@H]2C[C@H](O)[C@@H](COP(=O)(O)OP(=O)(…`
CHEMBL3229681	P09768	—	525.2 Da LogP -1.51 TPSA 273.2	3 viol.	✓ Clean	`CC(=O)Nc1cn([C@H]2C[C@H](O)[C@@H](COP(=O)(O)OP(…`
CHEMBL3229814	P09768	—	567.3 Da LogP -1.27 TPSA 273.2	3 viol.	✓ Clean	`CCC(=O)NCC(OP(=O)(O)OP(=O)(O)OP(=O)(O)O)[C@H]1O…`

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
ZINC13507072	1.000	482.2 Da LogP -1.16 TPSA 244.1	2 viol.	✓ Clean	`Cc1cn([C@@H]2C[C@@H](O)[C@H](CO[P@@](=O)(O)O[P@…`
ZINC1842580	1.000	242.2 Da LogP -1.51 TPSA 104.5	✓ Ro5	✓ Clean	`Cc1cn([C@@H]2C[C@H](O)[C@H](CO)O2)c(=O)[nH]c1=O`
ZINC2159	1.000	242.2 Da LogP -1.51 TPSA 104.5	✓ Ro5	✓ Clean	`Cc1cn([C@@H]2C[C@@H](O)[C@H](CO)O2)c(=O)[nH]c1=O`
ZINC2545102	1.000	242.2 Da LogP -1.51 TPSA 104.5	✓ Ro5	✓ Clean	`Cc1cn([C@H]2C[C@@H](O)[C@H](CO)O2)c(=O)[nH]c1=O`
ZINC25672	1.000	242.2 Da LogP -1.51 TPSA 104.5	✓ Ro5	✓ Clean	`Cc1cn([C@H]2C[C@H](O)[C@@H](CO)O2)c(=O)[nH]c1=O`
ZINC2572653	1.000	242.2 Da LogP -1.51 TPSA 104.5	✓ Ro5	✓ Clean	`Cc1cn([C@@H]2C[C@@H](O)[C@@H](CO)O2)c(=O)[nH]c1…`
ZINC3831529	1.000	242.2 Da LogP -1.51 TPSA 104.5	✓ Ro5	✓ Clean	`Cc1cn([C@H]2C[C@H](O)[C@H](CO)O2)c(=O)[nH]c1=O`
ZINC5765078	1.000	242.2 Da LogP -1.51 TPSA 104.5	✓ Ro5	✓ Clean	`Cc1cn([C@H]2C[C@@H](O)[C@@H](CO)O2)c(=O)[nH]c1=O`
ZINC6072455	1.000	242.2 Da LogP -1.51 TPSA 104.5	✓ Ro5	✓ Clean	`Cc1cn([C@@H]2C[C@H](O)[C@@H](CO)O2)c(=O)[nH]c1=O`
ZINC4804742	0.854	272.3 Da LogP -2.15 TPSA 124.8	✓ Ro5	✓ Clean	`Cc1cn([C@@H]2C[C@H](O)[C@H](O)[C@H](CO)O2)c(=O)…`
ZINC4804743	0.854	272.3 Da LogP -2.15 TPSA 124.8	✓ Ro5	✓ Clean	`Cc1cn([C@H]2C[C@H](O)[C@H](O)[C@H](CO)O2)c(=O)[…`
ZINC4804744	0.854	272.3 Da LogP -2.15 TPSA 124.8	✓ Ro5	✓ Clean	`Cc1cn([C@@H]2C[C@@H](O)[C@H](O)[C@H](CO)O2)c(=O…`
ZINC4804745	0.854	272.3 Da LogP -2.15 TPSA 124.8	✓ Ro5	✓ Clean	`Cc1cn([C@H]2C[C@@H](O)[C@H](O)[C@H](CO)O2)c(=O)…`
ZINC12360002	0.810	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	0.810	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	0.810	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	0.810	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	0.810	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	0.810	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	0.810	427.2 Da LogP -1.75 TPSA 232.6	2 viol.	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@@H](CO[P@@](=O)(O)OP(=…`
ZINC8586019	0.810	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	0.810	427.2 Da LogP -1.75 TPSA 232.6	2 viol.	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@@H](CO[P@@](=O)(O)OP(=…`
ZINC8586021	0.810	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	0.810	427.2 Da LogP -1.75 TPSA 232.6	2 viol.	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@@H](CO[P@@](=O)(O)OP(=…`
ZINC16928956	0.810	258.3 Da LogP -0.14 TPSA 87.5	✓ Ro5	✓ Clean	`Cc1cn([C@H]2C[C@@H](O)[C@@H](CO)O2)c(=O)[nH]c1=S`
ZINC5085194	0.805	244.2 Da LogP -0.54 TPSA 84.3	✓ Ro5	✓ Clean	`Cc1cn([C@@H]2C[C@H](O)[C@H](CF)O2)c(=O)[nH]c1=O`
ZINC5085195	0.805	244.2 Da LogP -0.54 TPSA 84.3	✓ Ro5	✓ Clean	`Cc1cn([C@H]2C[C@H](O)[C@H](CF)O2)c(=O)[nH]c1=O`
ZINC5085196	0.805	244.2 Da LogP -0.54 TPSA 84.3	✓ Ro5	✓ Clean	`Cc1cn([C@@H]2C[C@@H](O)[C@H](CF)O2)c(=O)[nH]c1=O`
ZINC5085197	0.805	244.2 Da LogP -0.54 TPSA 84.3	✓ Ro5	✓ Clean	`Cc1cn([C@H]2C[C@@H](O)[C@H](CF)O2)c(=O)[nH]c1=O`
ZINC11677083	0.791	244.2 Da LogP -0.54 TPSA 84.3	✓ Ro5	✓ Clean	`Cc1cn([C@@H]2C[C@@H](F)[C@@H](CO)O2)c(=O)[nH]c1…`
ZINC11677088	0.791	244.2 Da LogP -0.54 TPSA 84.3	✓ Ro5	✓ Clean	`Cc1cn([C@H]2C[C@@H](F)[C@@H](CO)O2)c(=O)[nH]c1=O`
ZINC1630862	0.791	255.3 Da LogP -1.29 TPSA 96.4	✓ Ro5	✓ Clean	`CN[C@@H]1C[C@H](n2cc(C)c(=O)[nH]c2=O)O[C@H]1CO`
ZINC17187167	0.791	241.2 Da LogP -1.55 TPSA 110.3	✓ Ro5	✓ Clean	`Cc1cn([C@@H]2C[C@@H](N)[C@@H](CO)O2)c(=O)[nH]c1…`
ZINC17187169	0.791	241.2 Da LogP -1.55 TPSA 110.3	✓ Ro5	✓ Clean	`Cc1cn([C@H]2C[C@@H](N)[C@@H](CO)O2)c(=O)[nH]c1=O`
ZINC17187171	0.791	241.2 Da LogP -1.55 TPSA 110.3	✓ Ro5	✓ Clean	`Cc1cn([C@@H]2C[C@H](N)[C@@H](CO)O2)c(=O)[nH]c1=O`
ZINC1725270	0.791	244.2 Da LogP -0.54 TPSA 84.3	✓ Ro5	✓ Clean	`Cc1cn([C@H]2C[C@H](F)[C@@H](CO)O2)c(=O)[nH]c1=O`
ZINC2130970	0.791	241.2 Da LogP -1.55 TPSA 110.3	✓ Ro5	✓ Clean	`Cc1cn([C@@H]2C[C@H](N)[C@H](CO)O2)c(=O)[nH]c1=O`
ZINC25054	0.791	244.2 Da LogP -0.54 TPSA 84.3	✓ Ro5	✓ Clean	`Cc1cn([C@H]2C[C@@H](F)[C@H](CO)O2)c(=O)[nH]c1=O`
ZINC3785451	0.791	244.2 Da LogP -0.54 TPSA 84.3	✓ Ro5	✓ Clean	`Cc1cn([C@@H]2C[C@H](F)[C@@H](CO)O2)c(=O)[nH]c1=O`
ZINC402630	0.791	241.2 Da LogP -1.55 TPSA 110.3	✓ Ro5	✓ Clean	`Cc1cn([C@@H]2C[C@@H](N)[C@H](CO)O2)c(=O)[nH]c1=O`
ZINC4537463	0.791	244.2 Da LogP -0.54 TPSA 84.3	✓ Ro5	✓ Clean	`Cc1cn([C@@H]2C[C@H](F)[C@H](CO)O2)c(=O)[nH]c1=O`
ZINC4537467	0.791	244.2 Da LogP -0.54 TPSA 84.3	✓ Ro5	✓ Clean	`Cc1cn([C@H]2C[C@H](F)[C@H](CO)O2)c(=O)[nH]c1=O`
ZINC56790	0.791	244.2 Da LogP -0.54 TPSA 84.3	✓ Ro5	✓ Clean	`Cc1cn([C@@H]2C[C@@H](F)[C@H](CO)O2)c(=O)[nH]c1=O`
ZINC5833725	0.791	255.3 Da LogP -1.29 TPSA 96.4	✓ Ro5	✓ Clean	`CN[C@H]1C[C@@H](n2cc(C)c(=O)[nH]c2=O)O[C@H]1CO`
ZINC5833727	0.791	255.3 Da LogP -1.29 TPSA 96.4	✓ Ro5	✓ Clean	`CN[C@H]1C[C@H](n2cc(C)c(=O)[nH]c2=O)O[C@H]1CO`
ZINC5833731	0.791	255.3 Da LogP -1.29 TPSA 96.4	✓ Ro5	✓ Clean	`CN[C@@H]1C[C@@H](n2cc(C)c(=O)[nH]c2=O)O[C@H]1CO`
ZINC6069509	0.791	241.2 Da LogP -1.55 TPSA 110.3	✓ Ro5	✓ Clean	`Cc1cn([C@H]2C[C@H](N)[C@@H](CO)O2)c(=O)[nH]c1=O`
ZINC6667024	0.791	256.3 Da LogP -0.86 TPSA 93.5	✓ Ro5	✓ Clean	`COC[C@H]1O[C@@H](n2cc(C)c(=O)[nH]c2=O)C[C@@H]1O`
ZINC4706616	0.786	258.3 Da LogP -0.58 TPSA 84.3	✓ Ro5	✓ Clean	`Cc1cn([C@@H]2C[C@H](O)[C@H](CS)O2)c(=O)[nH]c1=O`
ZINC5765073	0.786	241.2 Da LogP -1.55 TPSA 110.3	✓ Ro5	✓ Clean	`Cc1cn([C@H]2C[C@H](O)[C@@H](CN)O2)c(=O)[nH]c1=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.