Protein profile

VK055_1369

thymidylate kinase

Genome: KpATCC43816

Gene: tmk AIK79992.1 Structure source: AlphaFold + ColabFold UniProt A0A0H3GMT6

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Amino acids 213

Annotations 7

Features 15

PDB binders 9

Druggability 0.734

Overview

Basic information about this protein and its source genome.

Accession: VK055_1369
Assembly: Klebsiella pneumoniae subsp. pneumoniae strain ATCC 43816 KPPR1, complete genome
Gene: tmk AIK79992.1
Status: annotated
Amino acids: 213
Structure source: AlphaFold + ColabFold

2.7.4.9

GO:0005524 Binding to ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator. GO:0006233 The chemical reactions and pathways resulting in the formation of dTDP, deoxyribosylthymine diphosphate (2'-deoxyribosylthymine5'-diphosphate). GO:0004798 Catalysis of the reaction: dTMP + ATP = dTDP + ADP. GO:0005829 The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes. GO:0006235 The chemical reactions and pathways resulting in the formation of dTTP, deoxyribosylthymine triphosphate. GO:0006227 The chemical reactions and pathways resulting in the formation of dUDP, deoxyuridine diphosphate (2'-deoxy-5'-uridylyl phosphate).

Target profile

Computed evidence for target prioritization.

Human off-target: hit
Human identity (%): 29.353
Human E-value: 1.04e-09
Gut microbiome off-target: hit
Essential (DEG): Y
DEG identity (%): 85.446
DEG E-value: 8.770000000000001e-132
Localization: Cytoplasmic
ColabFold pLDDT: 96.72

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 0.734

Structure A0A0H3GMT6

Pocket Pocket 1

P2Rank 0.499

Structure A0A0H3GMT6

Pocket Pocket 1

ColabFold model

FPocket 0.697 · Pocket 1

P2Rank 0.445 · Pocket 1

Core conservation Conserved core gene

Roary core

CoreCruncher core

Gut microbiome 150 / 4744 genomes with a hit

Normalized 0.032

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)

2.7.4.9

Gene Ontology (GO)

GO:0005524 Binding to ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
GO:0006233 The chemical reactions and pathways resulting in the formation of dTDP, deoxyribosylthymine diphosphate (2'-deoxyribosylthymine5'-diphosphate).
GO:0004798 Catalysis of the reaction: dTMP + ATP = dTDP + ADP.
GO:0005829 The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
GO:0006235 The chemical reactions and pathways resulting in the formation of dTTP, deoxyribosylthymine triphosphate.
GO:0006227 The chemical reactions and pathways resulting in the formation of dUDP, deoxyuridine diphosphate (2'-deoxy-5'-uridylyl phosphate).

Sequence Features

Domain/signature hits from InterPro and related databases.

15 records

Show feature table

Start	End	DB	Term	Name
97	109	ProSitePatterns	PS01331	Thymidylate kinase signature.
97	109	InterPro	IPR018095	Thymidylate kinase, conserved site
1	212	Gene3D	G3DSA:3.40.50.300	-
1	212	InterPro	IPR027417	P-loop containing nucleoside triphosphate hydrolase
2	200	NCBIfam	TIGR00041	dTMP kinase
2	200	InterPro	IPR018094	Thymidylate kinase
5	206	CDD	cd01672	TMPK
1	213	FunFam	G3DSA:3.40.50.300:FF:000321	Thymidylate kinase
1	208	SUPERFAMILY	SSF52540	P-loop containing nucleoside triphosphate hydrolases
1	208	InterPro	IPR027417	P-loop containing nucleoside triphosphate hydrolase
4	208	Hamap	MF_00165	Thymidylate kinase [tmk].
4	208	InterPro	IPR018094	Thymidylate kinase
8	200	Pfam	PF02223	Thymidylate kinase
8	200	InterPro	IPR039430	Thymidylate kinase-like domain
3	209	PANTHER	PTHR10344	THYMIDYLATE 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_A0A0H3GMT6	AlphaFold	—	—	full sequence	—	Viewing
ColabFold VK055_1369	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				0.734

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				4.27	0.176
2				1.66	0.028

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				0.697
5				0.342

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	5.15	0.237
2	2.56	0.072
3	1.34	0.015

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.

61 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
0DF	3UWK	Q9HZN8	225.3 Da LogP 1.93 TPSA 50.7	✓ Ro5	✓ Clean	`CN1c2cc(cnc2NC1=O)c3ccccc3`
0DJ	3UWO	Q9HZN8	268.3 Da LogP 1.03 TPSA 93.8	✓ Ro5	✓ Clean	`CN1c2cc(cnc2NC1=O)c3cccc(c3)C(=O)N`
0DN	3UXM	Q9HZN8	244.2 Da LogP -0.54 TPSA 84.3	✓ Ro5	✓ Clean	`CC1=CN(C(=O)NC1=O)[C@H]2C[C@@H]([C@H](O2)CF)O`
ACP	5X8C	Q5SHX3	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)…`
ATM	4GMD	Q9HZN8	347.2 Da LogP -0.08 TPSA 179.6	✓ Ro5	Alert	`CC1=CN(C(=O)NC1=O)[C@H]2C[C@@H]([C@H](O2)COP(=O…`
T5A	4TMK	P0A720	891.4 Da LogP -1.86 TPSA 445.5	3 viol.	✓ Clean	`CC1=CN(C(=O)NC1=O)[C@H]2C[C@@H]([C@H](O2)CO[P@@…`
THM	4ESH	Q9HZN8	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`
TYD	5ZAX	Q5SHX3	402.2 Da LogP -1.28 TPSA 197.6	✓ Ro5	✓ Clean	`CC1=CN(C(=O)NC1=O)[C@H]2C[C@@H]([C@H](O2)CO[P@]…`
Z5A	5TMP	P0A720	911.3 Da LogP -3.71 TPSA 488.2	2 viol.	Alert	`CC1=CN(C(=O)NC1=O)[C@H]2C[C@@H]([C@H](O2)COP(=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).

Ligand	UniProt (homolog)	pchembl	MW · LogP · TPSA	Lipinski	PAINS	SMILES
08D	P0A720	—	253.3 Da LogP 1.37 TPSA 98.2	✓ Ro5	✓ Clean	`Cc1cc(no1)NS(=O)(=O)c2ccc(cc2)N`
FOM	P0A720	—	183.1 Da LogP -0.60 TPSA 98.1	✓ Ro5	✓ Clean	`C(CN(C=O)O)CP(=O)(O)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
ZINC12503817	1.000	347.2 Da LogP -0.08 TPSA 179.6	✓ Ro5	Alert	`Cc1cn([C@H]2C[C@H](N=[N+]=[N-])[C@@H](COP(=O)(O…`
ZINC5085194	1.000	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	1.000	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	1.000	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	1.000	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`
ZINC6756209	1.000	225.3 Da LogP 1.93 TPSA 50.7	✓ Ro5	✓ Clean	`Cn1c(=O)[nH]c2ncc(-c3ccccc3)cc21`
ZINC89763	1.000	253.3 Da LogP 1.37 TPSA 98.2	✓ Ro5	✓ Clean	`Cc1cc(NS(=O)(=O)c2ccc(N)cc2)no1`
ZINC77270915	0.889	408.5 Da LogP 2.17 TPSA 144.4	✓ Ro5	✓ Clean	`Cc1cc(NS(=O)(=O)c2ccc(NS(=O)(=O)c3ccc(N)cc3)cc2…`
ZINC1842580	0.805	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	0.805	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	0.805	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	0.805	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	0.805	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	0.805	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	0.805	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	0.805	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`
ZINC95882059	0.804	269.3 Da LogP 1.63 TPSA 88.0	✓ Ro5	✓ Clean	`Cn1c(=O)[nH]c2ncc(-c3cccc(C(=O)O)c3)cc21`
ZINC8559746	0.793	331.2 Da LogP 0.21 TPSA 159.4	✓ Ro5	Alert	`Cc1cn([C@H]2C[C@H](N=[N+]=[N-])[C@@H](CO[P@H](=…`
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`
ZINC4706617	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`
ZINC4706618	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`
ZINC4706619	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`
ZINC11592709	0.778	267.2 Da LogP -0.20 TPSA 133.1	✓ Ro5	Alert	`Cc1cn([C@@H]2C[C@@H](N=[N+]=[N-])[C@@H](CO)O2)c…`
ZINC3779042	0.778	267.2 Da LogP -0.20 TPSA 133.1	✓ Ro5	Alert	`Cc1cn([C@H]2C[C@H](N=[N+]=[N-])[C@@H](CO)O2)c(=…`
ZINC3831618	0.778	267.2 Da LogP -0.20 TPSA 133.1	✓ Ro5	Alert	`Cc1cn([C@@H]2C[C@H](N=[N+]=[N-])[C@H](CO)O2)c(=…`
ZINC3831619	0.778	267.2 Da LogP -0.20 TPSA 133.1	✓ Ro5	Alert	`Cc1cn([C@H]2C[C@H](N=[N+]=[N-])[C@H](CO)O2)c(=O…`
ZINC3831620	0.778	267.2 Da LogP -0.20 TPSA 133.1	✓ Ro5	Alert	`Cc1cn([C@@H]2C[C@@H](N=[N+]=[N-])[C@H](CO)O2)c(…`
ZINC3831621	0.778	267.2 Da LogP -0.20 TPSA 133.1	✓ Ro5	Alert	`Cc1cn([C@H]2C[C@@H](N=[N+]=[N-])[C@H](CO)O2)c(=…`
ZINC3978074	0.778	267.2 Da LogP -0.20 TPSA 133.1	✓ Ro5	Alert	`Cc1cn([C@@H]2C[C@H](N=[N+]=[N-])[C@@H](CO)O2)c(…`
ZINC4467870	0.778	267.2 Da LogP -0.20 TPSA 133.1	✓ Ro5	Alert	`Cc1cn([C@H]2C[C@@H](N=[N+]=[N-])[C@@H](CO)O2)c(…`
ZINC90951	0.771	252.3 Da LogP 2.09 TPSA 72.2	✓ Ro5	✓ Clean	`Cc1ccc(S(=O)(=O)Nc2cc(C)on2)cc1`
ZINC73314914	0.771	282.3 Da LogP 1.29 TPSA 79.8	✓ Ro5	✓ Clean	`CNC(=O)c1cccc(-c2cnc3[nH]c(=O)n(C)c3c2)c1`
ZINC73315496	0.765	325.3 Da LogP 0.14 TPSA 122.9	✓ Ro5	✓ Clean	`Cn1c(=O)[nH]c2ncc(-c3cccc(C(=O)NCC(N)=O)c3)cc21`
ZINC6667024	0.750	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`
ZINC74936874	0.750	316.4 Da LogP 1.19 TPSA 106.3	✓ Ro5	✓ Clean	`Cc1cc(NS(=O)(=O)c2ccc(S(C)(=O)=O)cc2)no1`
ZINC13523519	0.741	322.2 Da LogP -1.40 TPSA 151.1	✓ Ro5	✓ Clean	`Cc1cn([C@@H]2C[C@@H](O)[C@@H](COP(=O)(O)O)O2)c(…`
ZINC1532628	0.741	322.2 Da LogP -1.40 TPSA 151.1	✓ Ro5	✓ Clean	`Cc1cn([C@@H]2C[C@@H](O)[C@H](COP(=O)(O)O)O2)c(=…`
ZINC1678872	0.741	322.2 Da LogP -1.40 TPSA 151.1	✓ Ro5	✓ Clean	`Cc1cn([C@H]2C[C@H](O)[C@@H](COP(=O)(O)O)O2)c(=O…`
ZINC2047010	0.741	322.2 Da LogP -1.40 TPSA 151.1	✓ Ro5	✓ Clean	`Cc1cn([C@H]2C[C@@H](O)[C@H](COP(=O)(O)O)O2)c(=O…`
ZINC3870253	0.741	322.2 Da LogP -1.40 TPSA 151.1	✓ Ro5	✓ Clean	`Cc1cn([C@@H]2C[C@H](O)[C@H](COP(=O)(O)O)O2)c(=O…`
ZINC3870254	0.741	322.2 Da LogP -1.40 TPSA 151.1	✓ Ro5	✓ Clean	`Cc1cn([C@H]2C[C@H](O)[C@H](COP(=O)(O)O)O2)c(=O)…`
ZINC6523446	0.741	322.2 Da LogP -1.40 TPSA 151.1	✓ Ro5	✓ Clean	`Cc1cn([C@@H]2C[C@H](O)[C@@H](COP(=O)(O)O)O2)c(=…`
ZINC6416056	0.737	280.3 Da LogP 2.91 TPSA 72.2	✓ Ro5	✓ Clean	`Cc1cc(NS(=O)(=O)c2ccc(C(C)C)cc2)no1`
ZINC116196	0.730	256.3 Da LogP 1.92 TPSA 72.2	✓ Ro5	✓ Clean	`Cc1cc(NS(=O)(=O)c2ccc(F)cc2)no1`
ZINC31021	0.730	317.2 Da LogP 2.55 TPSA 72.2	✓ Ro5	✓ Clean	`Cc1cc(NS(=O)(=O)c2ccc(Br)cc2)no1`
ZINC90945	0.730	272.7 Da LogP 2.44 TPSA 72.2	✓ Ro5	✓ Clean	`Cc1cc(NS(=O)(=O)c2ccc(Cl)cc2)no1`
ZINC4804742	0.727	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	0.727	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	0.727	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)…`

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.