Protein profile

PA2962

thymidylate kinase

Genome: NC_002516.2

Gene: PA2962 tmk Structure source: Experimental + AlphaFold UniProt Q9HZN8

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Amino acids 210

Annotations 8

Features 13

PDB binders 12

Druggability 0.725

Overview

Basic information about this protein and its source genome.

Accession: PA2962
Assembly: Pseudomonas aeruginosa PAO1, complete genome
Gene: PA2962 tmk
Status: annotated
Amino acids: 210
Structure source: Experimental + AlphaFold

2.7.4.9

GO:0005737 The contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures. GO:0005829 The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes. GO:0005524 Binding to ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator. GO:0004798 Catalysis of the reaction: dTMP + ATP = dTDP + ADP. GO:0006233 The chemical reactions and pathways resulting in the formation of dTDP, deoxyribosylthymine diphosphate (2'-deoxyribosylthymine5'-diphosphate). GO:0006235 The chemical reactions and pathways resulting in the formation of dTTP, deoxyribosylthymine triphosphate.

Target profile

Computed evidence for target prioritization.

Human off-target: hit
Human identity (%): 26.531
Human E-value: 3e-08
Gut microbiome off-target: hit
Essential (DEG): Y
Localization: Cytoplasmic

Selected Druggability evidence

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 0.725

Structure –

Pocket –

Sequence

Primary amino-acid sequence viewer.

MTGLFVTLEGPEGAGKSTNRDYLAERLRERGIEVQLTREPGGTPLAERIRELLLAPSDEPMAADTELLLMFAARAQHLAGVIRPALARGAVVLCDRFTDATYAYQGGGRGLPEARIAALESFVQGDLRPDLTLVFDLPVEIGLARAAARGRLDRFEQEDRRFFEAVRQTYLQRAAQAPERYQVLDAGLPLAEVQAGLDRLLPNLLERLNG

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 7 GO

Enzyme Commission (EC)

2.7.4.9

Gene Ontology (GO)

GO:0005737 The contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
GO:0005829 The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
GO:0005524 Binding to ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
GO:0004798 Catalysis of the reaction: dTMP + ATP = dTDP + ADP.
GO:0006233 The chemical reactions and pathways resulting in the formation of dTDP, deoxyribosylthymine diphosphate (2'-deoxyribosylthymine5'-diphosphate).
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.

13 records

Show feature table

Start	End	DB	Term	Name
2	195	NCBIfam	TIGR00041	dTMP kinase
2	195	InterPro	IPR018094	Thymidylate kinase
3	201	PANTHER	PTHR10344	THYMIDYLATE KINASE
8	195	Pfam	PF02223	Thymidylate kinase
8	195	InterPro	IPR039430	Thymidylate kinase-like domain
1	207	SUPERFAMILY	SSF52540	P-loop containing nucleoside triphosphate hydrolases
1	207	InterPro	IPR027417	P-loop containing nucleoside triphosphate hydrolase
1	210	Gene3D	G3DSA:3.40.50.300	-
1	210	InterPro	IPR027417	P-loop containing nucleoside triphosphate hydrolase
4	201	CDD	cd01672	TMPK
1	210	FunFam	G3DSA:3.40.50.300:FF:000321	Thymidylate kinase
4	205	Hamap	MF_00165	Thymidylate kinase [tmk].
4	205	InterPro	IPR018094	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

7 + 1

Experimental PDB entries and predicted models. Click Switch to display a different structure in the viewer.

Entry	Method	Resolution	Chain	Coverage	Links	Status
PDB 4EDH	X-ray	1.32 Å	A,B	100.0% 1-210	PDBe RCSB PDBj File	Viewing
PDB 3UWO	X-ray	1.70 Å	A,B	100.0% 1-210	PDBe RCSB PDBj File	Loaded
PDB 4E5U	X-ray	1.81 Å	A,B	100.0% 1-210	PDBe RCSB PDBj File	Loaded
PDB 3UWK	X-ray	1.91 Å	A,B	100.0% 1-210	PDBe RCSB PDBj File	Loaded
PDB 4ESH	X-ray	1.95 Å	A	100.0% 1-210	PDBe RCSB PDBj File	Loaded
PDB 4GMD	X-ray	1.98 Å	A,B,C,D	100.0% 1-210	PDBe RCSB PDBj File	Loaded
PDB 3UXM	X-ray	1.95 Å	A,B,C,D	99.5% 2-210	PDBe RCSB PDBj File	Loaded
AlphaFold PA2962	AlphaFold	—	—	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				0.725

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	10.19	0.548
2	7.53	0.397
3	1.83	0.035
4	1.42	0.018

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
2				0.876
1				0.442

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.

Ligand	Source crystal	MW · LogP · TPSA	Lipinski	PAINS	SMILES
0DF	3UWK 1.91 Å Open crystal	225.3 Da LogP 1.93 TPSA 50.7	✓ Ro5	✓ Clean	`CN1c2cc(cnc2NC1=O)c3ccccc3`
0DJ	3UWO 1.70 Å Open crystal	268.3 Da LogP 1.03 TPSA 93.8	✓ Ro5	✓ Clean	`CN1c2cc(cnc2NC1=O)c3cccc(c3)C(=O)N`
0DN	3UXM 1.95 Å Open crystal	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`
ATM	4GMD 1.98 Å Open crystal	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…`
THM	4ESH 1.95 Å Open crystal	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`

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
0YB	4GFD	P65248	584.5 Da LogP 5.91 TPSA 104.6	2 viol.	✓ Clean	`CC1=CN(C(=O)NC1=O)[C@H]2CCCN(C2)[C@H](CC(C)(C)C…`
13Y	4HDC	P65249	526.0 Da LogP 5.41 TPSA 104.6	2 viol.	✓ Clean	`CC1=CN(C(=O)NC1=O)[C@H]2CCCN(C2)[C@H](CC(C)C)c3…`
14D	4HEJ	P65249	459.5 Da LogP 4.49 TPSA 67.3	✓ Ro5	✓ Clean	`CC1=CN(C(=O)NC1=O)[C@H]2CCCN(C2)Cc3cccc(c3)Oc4c…`
43N	4XWA	A7WYM2	589.1 Da LogP 5.85 TPSA 116.7	2 viol.	✓ Clean	`CCNc1cc(cc(c1C(=O)O)Oc2cccc(c2)Cl)[C@@H](c3cccc…`
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@@…`
TYD	3LV8	Q9KQI2	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)…`
ZINC4804744	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.