Protein profile

PA0904

aspartokinase

Genome: NC_002516.2

Gene: lysC PA0904 Structure source: Experimental + AlphaFold UniProt O69077

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Amino acids 412

Annotations 9

Features 36

PDB binders 0

Druggability 0.859

Overview

Basic information about this protein and its source genome.

Accession: PA0904
Assembly: Pseudomonas aeruginosa PAO1, complete genome
Gene: lysC PA0904
Status: annotated
Amino acids: 412
Structure source: Experimental + AlphaFold

2.7.2.4

GO:0005829 The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes. GO:0004072 Catalysis of the reaction: L-aspartate + ATP = 4-phospho-L-aspartate + ADP + H+. GO:0005524 Binding to ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator. GO:0019877 OBSOLETE. The chemical reactions and pathways resulting in the formation of diaminopimelate, both as an intermediate in lysine biosynthesis and as a component (as meso-diaminopimelate) of the peptidoglycan of Gram-negative bacterial cell walls. GO:0009090 The chemical reactions and pathways resulting in the formation of homoserine, alpha-amino-gamma-hydroxybutyric acid. GO:0009089 OBSOLETE. The chemical reactions and pathways resulting in the formation of lysine, via the intermediate diaminopimelate.

Target profile

Computed evidence for target prioritization.

Human off-target: No hit
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 0.859

Structure –

Pocket –

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)

2.7.2.4

Gene Ontology (GO)

GO:0005829 The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
GO:0004072 Catalysis of the reaction: L-aspartate + ATP = 4-phospho-L-aspartate + ADP + H+.
GO:0005524 Binding to ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
GO:0019877 OBSOLETE. The chemical reactions and pathways resulting in the formation of diaminopimelate, both as an intermediate in lysine biosynthesis and as a component (as meso-diaminopimelate) of the peptidoglycan of Gram-negative bacterial cell walls.
GO:0009090 The chemical reactions and pathways resulting in the formation of homoserine, alpha-amino-gamma-hydroxybutyric acid.
GO:0009089 OBSOLETE. The chemical reactions and pathways resulting in the formation of lysine, via the intermediate diaminopimelate.
GO:0009088 The chemical reactions and pathways resulting in the formation of L-threonine (2-amino-3-hydroxybutyric acid), a polar, uncharged, essential amino acid found in peptide linkage in proteins.
GO:0008652 The chemical reactions and pathways resulting in the formation of amino acids, organic acids containing one or more amino substituents.

Sequence Features

Domain/signature hits from InterPro and related databases.

36 records

Show feature table

Start	End	DB	Term	Name
253	412	FunFam	G3DSA:3.30.2130.10:FF:000002	Aspartokinase
5	13	ProSitePatterns	PS00324	Aspartokinase signature.
5	13	InterPro	IPR018042	Aspartate kinase, conserved site
1	402	PANTHER	PTHR21499	ASPARTATE KINASE
342	404	CDD	cd04923	ACT_AK-LysC-DapG-like_2
57	411	PIRSF	PIRSF000726	Asp_kin
57	411	InterPro	IPR005260	Aspartate kinase, monofunctional class
1	62	PIRSF	PIRSF000726	Asp_kin
1	62	InterPro	IPR005260	Aspartate kinase, monofunctional class
254	412	Gene3D	G3DSA:3.30.2130.10	-
266	340	ProSiteProfiles	PS51671	ACT domain profile.
266	340	InterPro	IPR002912	ACT domain
4	241	SUPERFAMILY	SSF53633	Carbamate kinase-like
4	241	InterPro	IPR036393	Acetylglutamate kinase-like superfamily
346	412	ProSiteProfiles	PS51671	ACT domain profile.
346	412	InterPro	IPR002912	ACT domain
263	337	CDD	cd04913	ACT_AKii-LysC-BS-like_1
3	229	Pfam	PF00696	Amino acid kinase family
3	229	InterPro	IPR001048	Aspartate/glutamate/uridylate kinase
332	405	SUPERFAMILY	SSF55021	ACT-like
332	405	InterPro	IPR045865	ACT-like domain
3	241	CDD	cd04261	AAK_AKii-LysC-BS
3	241	InterPro	IPR041740	Aspartokinase catalytic domain
63	403	NCBIfam	TIGR00657	aspartate kinase
63	403	InterPro	IPR001341	Aspartate kinase
339	399	Pfam	PF13840	ACT domain
339	399	InterPro	IPR027795	CASTOR, ACT domain
268	325	Pfam	PF01842	ACT domain
268	325	InterPro	IPR002912	ACT domain
1	254	FunFam	G3DSA:3.40.1160.10:FF:000002	Aspartokinase
1	253	Gene3D	G3DSA:3.40.1160.10	-
1	253	InterPro	IPR036393	Acetylglutamate kinase-like superfamily
1	404	NCBIfam	TIGR00656	aspartate kinase, monofunctional class
1	404	InterPro	IPR005260	Aspartate kinase, monofunctional class
249	327	SUPERFAMILY	SSF55021	ACT-like
249	327	InterPro	IPR045865	ACT-like domain

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

1 + 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 5YEI	X-ray	2.30 Å	A,C,E,G	100.0% 1-412	PDBe RCSB PDBj File	Viewing
AlphaFold PA0904	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
7				0.858
2				0.347

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	10.16	0.546
2	3.16	0.107
3	2.07	0.046

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				0.297

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.

32 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.

No PDB ligands found through similar proteins.

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
ZINC1709621	0.600	248.2 Da LogP -2.17 TPSA 167.0	✓ Ro5	✓ Clean	`N[C@@H](CC(=O)N[C@@H](CC(=O)O)C(=O)O)C(=O)O`
ZINC1709622	0.600	248.2 Da LogP -2.17 TPSA 167.0	✓ Ro5	✓ Clean	`N[C@H](CC(=O)N[C@@H](CC(=O)O)C(=O)O)C(=O)O`
ZINC1709623	0.600	248.2 Da LogP -2.17 TPSA 167.0	✓ Ro5	✓ Clean	`N[C@@H](CC(=O)N[C@H](CC(=O)O)C(=O)O)C(=O)O`
ZINC1709624	0.600	248.2 Da LogP -2.17 TPSA 167.0	✓ Ro5	✓ Clean	`N[C@H](CC(=O)N[C@H](CC(=O)O)C(=O)O)C(=O)O`
ZINC1575288	0.560	248.2 Da LogP -2.17 TPSA 167.0	✓ Ro5	✓ Clean	`N[C@@H](CC(=O)O)C(=O)N[C@@H](CC(=O)O)C(=O)O`
ZINC1575289	0.560	248.2 Da LogP -2.17 TPSA 167.0	✓ Ro5	✓ Clean	`N[C@H](CC(=O)O)C(=O)N[C@@H](CC(=O)O)C(=O)O`
ZINC1575290	0.560	248.2 Da LogP -2.17 TPSA 167.0	✓ Ro5	✓ Clean	`N[C@@H](CC(=O)O)C(=O)N[C@H](CC(=O)O)C(=O)O`
ZINC1575291	0.560	248.2 Da LogP -2.17 TPSA 167.0	✓ Ro5	✓ Clean	`N[C@H](CC(=O)O)C(=O)N[C@H](CC(=O)O)C(=O)O`
ZINC5131760	0.560	237.2 Da LogP -0.94 TPSA 137.9	✓ Ro5	✓ Clean	`N[C@@H](CS[C@@H](CC(=O)O)C(=O)O)C(=O)O`
ZINC5131761	0.560	237.2 Da LogP -0.94 TPSA 137.9	✓ Ro5	✓ Clean	`N[C@H](CS[C@@H](CC(=O)O)C(=O)O)C(=O)O`
ZINC5131922	0.560	237.2 Da LogP -0.94 TPSA 137.9	✓ Ro5	✓ Clean	`N[C@@H](CS[C@H](CC(=O)O)C(=O)O)C(=O)O`
ZINC5131923	0.560	237.2 Da LogP -0.94 TPSA 137.9	✓ Ro5	✓ Clean	`N[C@H](CS[C@H](CC(=O)O)C(=O)O)C(=O)O`
ZINC100655912	0.519	478.4 Da LogP -4.25 TPSA 299.8	1 viol.	✓ Clean	`N[C@H](CC(=O)O)C(=O)N[C@H](CC(=O)O)C(=O)N[C@H](…`
ZINC100655916	0.519	478.4 Da LogP -4.25 TPSA 299.8	1 viol.	✓ Clean	`N[C@H](CC(=O)O)C(=O)N[C@H](CC(=O)O)C(=O)N[C@@H]…`
ZINC255993703	0.519	478.4 Da LogP -4.25 TPSA 299.8	1 viol.	✓ Clean	`N[C@H](CC(=O)O)C(=O)N[C@H](CC(=O)O)C(=O)N[C@H](…`
ZINC2568071	0.519	218.3 Da LogP -1.08 TPSA 112.7	✓ Ro5	✓ Clean	`CC(C)[C@H](NC(=O)[C@@H](N)[C@@H](C)O)C(=O)O`
ZINC4533843	0.519	363.3 Da LogP -3.21 TPSA 233.4	1 viol.	✓ Clean	`N[C@@H](CC(=O)O)C(=O)N[C@@H](CC(=O)O)C(=O)N[C@@…`
ZINC4533848	0.519	478.4 Da LogP -4.25 TPSA 299.8	1 viol.	✓ Clean	`N[C@@H](CC(=O)O)C(=O)N[C@@H](CC(=O)O)C(=O)N[C@@…`
ZINC4533853	0.519	478.4 Da LogP -4.25 TPSA 299.8	1 viol.	✓ Clean	`N[C@H](CC(=O)O)C(=O)N[C@H](CC(=O)O)C(=O)N[C@@H]…`
ZINC1577651	0.500	234.2 Da LogP -0.66 TPSA 149.2	✓ Ro5	✓ Clean	`O=C(O)C[C@H](C(=O)O)[C@@H](CC(=O)O)C(=O)O`
ZINC1577652	0.500	234.2 Da LogP -0.66 TPSA 149.2	✓ Ro5	✓ Clean	`O=C(O)C[C@@H](C(=O)O)[C@@H](CC(=O)O)C(=O)O`
ZINC1577653	0.500	234.2 Da LogP -0.66 TPSA 149.2	✓ Ro5	✓ Clean	`O=C(O)C[C@H](C(=O)O)[C@H](CC(=O)O)C(=O)O`
ZINC22923898	0.500	307.3 Da LogP -3.04 TPSA 199.3	1 viol.	✓ Clean	`N[C@@H](CN[C@@H](CN[C@@H](CC(=O)O)C(=O)O)C(=O)O…`
ZINC22923905	0.500	307.3 Da LogP -3.04 TPSA 199.3	1 viol.	✓ Clean	`N[C@@H](CN[C@H](CN[C@@H](CC(=O)O)C(=O)O)C(=O)O)…`
ZINC22930737	0.500	307.3 Da LogP -3.04 TPSA 199.3	1 viol.	✓ Clean	`N[C@H](CN[C@H](CN[C@@H](CC(=O)O)C(=O)O)C(=O)O)C…`
ZINC23355305	0.500	307.3 Da LogP -3.04 TPSA 199.3	1 viol.	✓ Clean	`N[C@H](CN[C@@H](CN[C@@H](CC(=O)O)C(=O)O)C(=O)O)…`
ZINC2560328	0.500	239.1 Da LogP 1.53 TPSA 63.3	✓ Ro5	✓ Clean	`N[C@@H](CC(C(F)(F)F)C(F)(F)F)C(=O)O`
ZINC2561115	0.500	321.3 Da LogP -3.49 TPSA 182.2	1 viol.	✓ Clean	`C[C@@H](O)[C@H](N)C(=O)N[C@H](C(=O)N[C@H](C(=O)…`
ZINC4348166	0.500	239.1 Da LogP 1.53 TPSA 63.3	✓ Ro5	✓ Clean	`N[C@H](CC(C(F)(F)F)C(F)(F)F)C(=O)O`
ZINC5462352	0.500	321.3 Da LogP -3.49 TPSA 182.2	1 viol.	✓ Clean	`C[C@H](O)[C@H](N)C(=O)N[C@H](C(=O)N[C@H](C(=O)O…`
ZINC5462358	0.500	321.3 Da LogP -3.49 TPSA 182.2	1 viol.	✓ Clean	`C[C@H](O)[C@@H](N)C(=O)N[C@H](C(=O)N[C@H](C(=O)…`
ZINC5462362	0.500	321.3 Da LogP -3.49 TPSA 182.2	1 viol.	✓ Clean	`C[C@@H](O)[C@H](NC(=O)[C@@H](NC(=O)[C@H](N)[C@@…`

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.