Protein profile

KP13_00360

Lysine-sensitive aspartokinase 3

Genome: KpKP13

Gene: lysC AHE46901.1 Structure source: AlphaFold + ColabFold UniProt A0A0H3GQ40

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Amino acids 449

Annotations 8

Features 33

PDB binders 1

Druggability 0.596

Overview

Basic information about this protein and its source genome.

Accession: KP13_00360
Assembly: Klebsiella pneumoniae subsp. pneumoniae Kp13, complete sequence
Gene: lysC AHE46901.1
Status: annotated
Amino acids: 449
Structure source: AlphaFold + ColabFold

2.7.2.4

GO:0009089 OBSOLETE. The chemical reactions and pathways resulting in the formation of lysine, via the intermediate diaminopimelate. GO:0004072 Catalysis of the reaction: L-aspartate + ATP = 4-phospho-L-aspartate + ADP + H+. GO:0008652 The chemical reactions and pathways resulting in the formation of amino acids, organic acids containing one or more amino substituents. 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:0009090 The chemical reactions and pathways resulting in the formation of homoserine, alpha-amino-gamma-hydroxybutyric acid.

Target profile

Computed evidence for target prioritization.

Human off-target: No hit
Human identity (%): 0.0
Gut microbiome off-target: hit
Essential (DEG): N
DEG identity (%): 0.0
Localization: Cytoplasmic
ColabFold pLDDT: 92.45

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 0.596

Structure A0A0H3GQ40

Pocket Pocket 1

P2Rank 0.732

Structure A0A0H3GQ40

Pocket Pocket 1

ColabFold model

FPocket 0.677 · Pocket 1

P2Rank 0.653 · Pocket 1

Core conservation Conserved core gene

Roary core

CoreCruncher core

Gut microbiome 155 / 4744 genomes with a hit

Normalized 0.033

Sequence

Primary amino-acid sequence viewer.

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 7 GO

Enzyme Commission (EC)

2.7.2.4

Gene Ontology (GO)

GO:0009089 OBSOLETE. The chemical reactions and pathways resulting in the formation of lysine, via the intermediate diaminopimelate.
GO:0004072 Catalysis of the reaction: L-aspartate + ATP = 4-phospho-L-aspartate + ADP + H+.
GO:0008652 The chemical reactions and pathways resulting in the formation of amino acids, organic acids containing one or more amino substituents.
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:0009090 The chemical reactions and pathways resulting in the formation of homoserine, alpha-amino-gamma-hydroxybutyric acid.
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.

Sequence Features

Domain/signature hits from InterPro and related databases.

33 records

Show feature table

Start	End	DB	Term	Name
6	14	ProSitePatterns	PS00324	Aspartokinase signature.
6	14	InterPro	IPR018042	Aspartate kinase, conserved site
3	449	NCBIfam	TIGR00657	aspartate kinase
3	449	InterPro	IPR001341	Aspartate kinase
4	291	SUPERFAMILY	SSF53633	Carbamate kinase-like
4	291	InterPro	IPR036393	Acetylglutamate kinase-like superfamily
2	449	PIRSF	PIRSF000726	Asp_kin
2	449	InterPro	IPR005260	Aspartate kinase, monofunctional class
42	134	Gene3D	G3DSA:1.20.120.1320	Aspartokinase, catalytic domain
42	134	InterPro	IPR042199	Aspartokinase/Bifunctional aspartokinase/homoserine dehydrogenase, catalytic domain
4	277	Pfam	PF00696	Amino acid kinase family
4	277	InterPro	IPR001048	Aspartate/glutamate/uridylate kinase
6	289	Gene3D	G3DSA:3.40.1160.10	-
6	289	InterPro	IPR036393	Acetylglutamate kinase-like superfamily
323	377	Pfam	PF01842	ACT domain
323	377	InterPro	IPR002912	ACT domain
386	449	CDD	cd04917	ACT_AKiii-LysC-EC_2
377	448	SUPERFAMILY	SSF55021	ACT-like
377	448	InterPro	IPR045865	ACT-like domain
309	383	Gene3D	G3DSA:3.30.70.260	-
308	384	CDD	cd04932	ACT_AKiii-LysC-EC_1
297	393	SUPERFAMILY	SSF55021	ACT-like
297	393	InterPro	IPR045865	ACT-like domain
301	448	Gene3D	G3DSA:3.30.70.260	-
309	379	FunFam	G3DSA:3.30.70.260:FF:000017	Aspartokinase
1	449	PANTHER	PTHR21499	ASPARTATE KINASE
4	290	CDD	cd04258	AAK_AKiii-LysC-EC
4	290	InterPro	IPR041745	Lysine-sensitive aspartokinase 3, N-terminal catalytic domain
313	394	ProSiteProfiles	PS51671	ACT domain profile.
313	394	InterPro	IPR002912	ACT domain
380	448	FunFam	G3DSA:3.30.70.260:FF:000023	Aspartokinase
3	449	NCBIfam	TIGR00656	aspartate kinase, monofunctional class
3	449	InterPro	IPR005260	Aspartate kinase, monofunctional class

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_A0A0H3GQ40	AlphaFold	—	—	full sequence	—	Viewing
ColabFold KP13_00360	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				0.596
22				0.008
13				0.001
25				0.001

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	17.63	0.732
2	4.79	0.175
3	4.09	0.135
4	2.23	0.045

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				0.677

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	7.44	0.39
2	3.33	0.118
3	2.92	0.094

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.

51 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
TAR	2CDQ	Q9LYU8	150.1 Da LogP -2.12 TPSA 115.1	✓ Ro5	✓ Clean	`[C@H]([C@@H](C(=O)O)O)(C(=O)O)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).

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`
ZINC1560405156	0.588	208.1 Da LogP -1.79 TPSA 155.5	1 viol.	✓ Clean	`O=C(O)/C(O)=C(\O)[C@H](O)[C@H](O)C(=O)O`
ZINC1560405157	0.588	208.1 Da LogP -1.79 TPSA 155.5	1 viol.	✓ Clean	`O=C(O)/C(O)=C(/O)[C@H](O)[C@H](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`
ZINC2123927	0.538	204.2 Da LogP -1.62 TPSA 129.7	✓ Ro5	✓ Clean	`C[C@H](NC(=O)[C@@H](N)CC(=O)O)C(=O)O`
ZINC2560978	0.538	204.2 Da LogP -1.62 TPSA 129.7	✓ Ro5	✓ Clean	`C[C@H](NC(=O)C[C@H](N)C(=O)O)C(=O)O`
ZINC1730666	0.524	208.2 Da LogP -1.46 TPSA 126.6	✓ Ro5	✓ Clean	`N[C@@H](CSC[C@H](N)C(=O)O)C(=O)O`
ZINC1730667	0.524	208.2 Da LogP -1.46 TPSA 126.6	✓ Ro5	✓ Clean	`N[C@H](CSC[C@H](N)C(=O)O)C(=O)O`
ZINC1730669	0.524	208.2 Da LogP -1.46 TPSA 126.6	✓ Ro5	✓ Clean	`N[C@H](CSC[C@@H](N)C(=O)O)C(=O)O`
ZINC3055005	0.524	204.2 Da LogP -0.63 TPSA 126.6	✓ Ro5	✓ Clean	`N[C@@H](CCCC[C@H](N)C(=O)O)C(=O)O`
ZINC3055007	0.524	204.2 Da LogP -0.63 TPSA 126.6	✓ Ro5	✓ Clean	`N[C@@H](CCCC[C@@H](N)C(=O)O)C(=O)O`
ZINC3055010	0.524	204.2 Da LogP -0.63 TPSA 126.6	✓ Ro5	✓ Clean	`N[C@H](CCCC[C@@H](N)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]…`
ZINC1529331	0.500	206.1 Da LogP -2.21 TPSA 149.2	✓ Ro5	✓ Clean	`O=C(O)C(=O)[C@H](C(=O)O)[C@@H](O)C(=O)O`
ZINC1529332	0.500	206.1 Da LogP -2.21 TPSA 149.2	✓ Ro5	✓ Clean	`O=C(O)C(=O)[C@H](C(=O)O)[C@H](O)C(=O)O`
ZINC1529333	0.500	206.1 Da LogP -2.21 TPSA 149.2	✓ Ro5	✓ Clean	`O=C(O)C(=O)[C@@H](C(=O)O)[C@@H](O)C(=O)O`
ZINC1529334	0.500	206.1 Da LogP -2.21 TPSA 149.2	✓ Ro5	✓ Clean	`O=C(O)C(=O)[C@@H](C(=O)O)[C@H](O)C(=O)O`
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`
ZINC1720127	0.500	218.3 Da LogP -0.24 TPSA 126.6	✓ Ro5	✓ Clean	`N[C@@H](CCCCC[C@H](N)C(=O)O)C(=O)O`
ZINC1720128	0.500	218.3 Da LogP -0.24 TPSA 126.6	✓ Ro5	✓ Clean	`N[C@@H](CCCCC[C@@H](N)C(=O)O)C(=O)O`
ZINC1720130	0.500	218.3 Da LogP -0.24 TPSA 126.6	✓ Ro5	✓ Clean	`N[C@H](CCCCC[C@@H](N)C(=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…`
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)…`
ZINC2384839	0.500	232.2 Da LogP -0.99 TPSA 129.7	✓ Ro5	✓ Clean	`CC(C)[C@H](NC(=O)[C@@H](N)CC(=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`
ZINC4580676	0.500	202.2 Da LogP -0.85 TPSA 126.6	✓ Ro5	✓ Clean	`N[C@H](C/C=C/C[C@@H](N)C(=O)O)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.