Protein profile

KP13_02141

Glutamate 5-kinase

Genome: KpKP13

Gene: AHE46147.1 proB Structure source: AlphaFold + ColabFold UniProt A0A0H3GK38

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Amino acids 367

Annotations 9

Features 41

PDB binders 4

Druggability 0.29

Overview

Basic information about this protein and its source genome.

Accession: KP13_02141
Assembly: Klebsiella pneumoniae subsp. pneumoniae Kp13, complete sequence
Gene: AHE46147.1 proB
Status: annotated
Amino acids: 367
Structure source: AlphaFold + ColabFold

2.7.2.11

GO:0005737 The contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures. GO:0006561 OBSOLETE. The chemical reactions and pathways resulting in the formation of proline (pyrrolidine-2-carboxylic acid), a chiral, cyclic, nonessential alpha-amino acid found in peptide linkage in proteins. GO:0016301 Catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule. GO:0003723 Binding to an RNA molecule or a portion thereof. GO:0004349 Catalysis of the reaction: L-glutamate + ATP = L-glutamyl 5-phosphate + ADP + H+. GO:0005524 Binding to ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.

Target profile

Computed evidence for target prioritization.

Human off-target: hit
Human identity (%): 33.448
Human E-value: 3.3300000000000003e-32
Gut microbiome off-target: hit
Essential (DEG): Y
DEG identity (%): 43.014
DEG E-value: 1.1699999999999999e-91
Localization: Cytoplasmic
ColabFold pLDDT: 92.53

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 0.29

Structure A0A0H3GK38

Pocket Pocket 25

P2Rank 0.872

Structure A0A0H3GK38

Pocket Pocket 1

ColabFold model

FPocket 0.191 · Pocket 5

P2Rank 0.863 · Pocket 1

Core conservation Conserved core gene

Roary core

CoreCruncher core

Gut microbiome 157 / 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 8 GO

Enzyme Commission (EC)

2.7.2.11

Gene Ontology (GO)

GO:0005737 The contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
GO:0006561 OBSOLETE. The chemical reactions and pathways resulting in the formation of proline (pyrrolidine-2-carboxylic acid), a chiral, cyclic, nonessential alpha-amino acid found in peptide linkage in proteins.
GO:0016301 Catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule.
GO:0003723 Binding to an RNA molecule or a portion thereof.
GO:0004349 Catalysis of the reaction: L-glutamate + ATP = L-glutamyl 5-phosphate + ADP + H+.
GO:0005524 Binding to ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
GO:0005829 The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
GO:0055129 The chemical reactions and pathways resulting in the formation of L-proline, an L-enantiomer of a chiral, cyclic, nonessential alpha-amino acid found in peptide linkage in proteins.

Sequence Features

Domain/signature hits from InterPro and related databases.

41 records

Show feature table

Start	End	DB	Term	Name
276	366	SUPERFAMILY	SSF88697	PUA domain-like
276	366	InterPro	IPR015947	PUA-like superfamily
76	104	PRINTS	PR00474	Glutamate 5-kinase family signature
76	104	InterPro	IPR001057	Glutamate/acetylglutamate kinase
148	175	PRINTS	PR00474	Glutamate 5-kinase family signature
148	175	InterPro	IPR001057	Glutamate/acetylglutamate kinase
209	229	PRINTS	PR00474	Glutamate 5-kinase family signature
209	229	InterPro	IPR001057	Glutamate/acetylglutamate kinase
42	56	PRINTS	PR00474	Glutamate 5-kinase family signature
42	56	InterPro	IPR001057	Glutamate/acetylglutamate kinase
116	137	PRINTS	PR00474	Glutamate 5-kinase family signature
116	137	InterPro	IPR001057	Glutamate/acetylglutamate kinase
276	359	SMART	SM00359	pua_5
276	359	InterPro	IPR002478	PUA domain
1	367	PIRSF	PIRSF000729	GK
1	367	InterPro	IPR011529	Glutamate 5-kinase
2	196	Gene3D	G3DSA:3.40.1160.10	-
2	196	InterPro	IPR036393	Acetylglutamate kinase-like superfamily
197	269	Gene3D	G3DSA:3.40.1160.10	-
197	269	InterPro	IPR036393	Acetylglutamate kinase-like superfamily
270	366	Gene3D	G3DSA:2.30.130.10	PUA domain
270	366	InterPro	IPR036974	PUA domain superfamily
1	273	FunFam	G3DSA:3.40.1160.10:FF:000006	Glutamate 5-kinase
3	354	PANTHER	PTHR43654	GLUTAMATE 5-KINASE
270	367	FunFam	G3DSA:2.30.130.10:FF:000003	Glutamate 5-kinase
6	234	Pfam	PF00696	Amino acid kinase family
6	234	InterPro	IPR001048	Aspartate/glutamate/uridylate kinase
5	259	Hamap	MF_00456	Glutamate 5-kinase [proB].
5	259	InterPro	IPR005715	Glutamate 5-kinase/delta-1-pyrroline-5-carboxylate synthase
5	366	NCBIfam	TIGR01027	glutamate 5-kinase
5	366	InterPro	IPR005715	Glutamate 5-kinase/delta-1-pyrroline-5-carboxylate synthase
276	350	Pfam	PF01472	PUA domain
276	350	InterPro	IPR002478	PUA domain
6	256	CDD	cd04242	AAK_G5K_ProB
6	256	InterPro	IPR041739	Glutamate-5-kinase domain
6	256	SUPERFAMILY	SSF53633	Carbamate kinase-like
6	256	InterPro	IPR036393	Acetylglutamate kinase-like superfamily
207	224	ProSitePatterns	PS00902	Glutamate 5-kinase signature.
207	224	InterPro	IPR019797	Glutamate 5-kinase, conserved site
275	353	ProSiteProfiles	PS50890	PUA domain profile.
264	366	CDD	cd21157	PUA_G5K

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_A0A0H3GK38	AlphaFold	—	—	full sequence	—	Viewing
ColabFold KP13_02141	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
25				0.29

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	7.23	0.376
2	4.78	0.212
3	3.69	0.14
4	1.54	0.023
5	0.96	0.005

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	12.56	0.655
2	4.56	0.196
3	2.43	0.066

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.

54 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
ANP	2BRI	Q8U122	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)…`
IP8	7LNU	M9SEQ1	166.1 Da LogP 1.06 TPSA 66.8	✓ Ro5	✓ Clean	`CC(=C)CCOP(=O)(O)O`
IPE	7LNU	M9SEQ1	246.1 Da LogP 1.18 TPSA 113.3	✓ Ro5	✓ Clean	`CC(=C)CCO[P@@](=O)(O)OP(=O)(O)O`
WZT	7LNT	M9SEQ1	188.1 Da LogP 1.30 TPSA 66.8	✓ Ro5	✓ Clean	`c1ccc(cc1)COP(=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
ZINC8215654	1.000	246.1 Da LogP 1.18 TPSA 113.3	✓ Ro5	✓ Clean	`C=C(C)CCO[P@@](=O)(O)OP(=O)(O)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(=…`
ZINC1655964	0.760	278.2 Da LogP 3.52 TPSA 55.8	✓ Ro5	✓ Clean	`O=P(O)(OCc1ccccc1)OCc1ccccc1`
ZINC13518964	0.741	347.2 Da LogP -1.86 TPSA 186.1	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@@H](COP(=O)(O)O)[C@H](…`
ZINC1532515	0.741	347.2 Da LogP -1.86 TPSA 186.1	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@H]1O[C@@H](COP(=O)(O)O)[C@H](O…`
ZINC1571045	0.741	347.2 Da LogP -1.86 TPSA 186.1	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@@H](COP(=O)(O)O)[C@@H]…`
ZINC1842158	0.741	347.2 Da LogP -1.86 TPSA 186.1	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@H]1O[C@@H](COP(=O)(O)O)[C@H](O…`
ZINC2046931	0.741	347.2 Da LogP -1.86 TPSA 186.1	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@@H](COP(=O)(O)O)[C@H](…`
ZINC2126310	0.741	347.2 Da LogP -1.86 TPSA 186.1	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@H](COP(=O)(O)O)[C@@H](…`
ZINC3201891	0.741	347.2 Da LogP -1.86 TPSA 186.1	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@@H](COP(=O)(O)O)[C@@H]…`
ZINC3201893	0.741	347.2 Da LogP -1.86 TPSA 186.1	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@H]1O[C@@H](COP(=O)(O)O)[C@@H](…`
ZINC3830180	0.741	347.2 Da LogP -1.86 TPSA 186.1	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@H]1O[C@@H](COP(=O)(O)O)[C@@H](…`
ZINC3860156	0.741	347.2 Da LogP -1.86 TPSA 186.1	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@H](COP(=O)(O)O)[C@@H](…`
ZINC3977897	0.741	347.2 Da LogP -1.86 TPSA 186.1	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@H]1O[C@H](COP(=O)(O)O)[C@@H](O…`
ZINC4806442	0.741	347.2 Da LogP -1.86 TPSA 186.1	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@H](COP(=O)(O)O)[C@H](O…`
ZINC8613167	0.741	347.2 Da LogP -1.86 TPSA 186.1	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@H](COP(=O)(O)O)[C@H](O…`
ZINC4096224	0.729	346.2 Da LogP -1.90 TPSA 191.9	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@H](CO[P@](N)(=O)O)[C@@…`
ZINC12503850	0.726	427.3 Da LogP -2.04 TPSA 229.4	1 viol.	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@H](CO[P@](=O)(O)OS(=O)…`
ZINC141161066	0.726	427.3 Da LogP -2.04 TPSA 229.4	1 viol.	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@H](CO[P@](=O)(O)OS(=O)…`
ZINC141163786	0.726	427.3 Da LogP -2.04 TPSA 229.4	1 viol.	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@H](CO[P@](=O)(O)OS(=O)…`
ZINC4228246	0.726	427.3 Da LogP -2.04 TPSA 229.4	1 viol.	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@H](CO[P@@](=O)(O)OS(=O…`
ZINC105372833	0.712	345.3 Da LogP -1.93 TPSA 197.6	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@H](COP(N)(N)=O)[C@H](O…`
ZINC105372837	0.712	345.3 Da LogP -1.93 TPSA 197.6	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@H](COP(N)(N)=O)[C@H](O…`
ZINC17107643	0.712	345.3 Da LogP -1.93 TPSA 197.6	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@H](COP(N)(N)=O)[C@@H](…`
ZINC204538551	0.712	345.3 Da LogP -1.93 TPSA 197.6	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@H](COP(N)(N)=O)[C@@H](…`
ZINC31475423	0.703	434.3 Da LogP -2.99 TPSA 238.4	2 viol.	✓ Clean	`Nc1ncnc2c1ncn2[C@H]1O[C@H](CO[P@@](=O)(O)OC(=O)…`
ZINC105469665	0.694	425.2 Da LogP -1.64 TPSA 223.4	2 viol.	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@H](CO[P@@](=O)(O)CP(=O…`
ZINC13527614	0.694	425.2 Da LogP -1.64 TPSA 223.4	2 viol.	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@H](CO[P@](=O)(O)CP(=O)…`
ZINC219330894	0.694	425.2 Da LogP -1.64 TPSA 223.4	2 viol.	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@H](CO[P@](=O)(O)CP(=O)…`
ZINC3873852	0.694	425.2 Da LogP -1.64 TPSA 223.4	2 viol.	✓ Clean	`Nc1ncnc2c1ncn2[C@H]1O[C@@H](CO[P@](=O)(O)CP(=O)…`
ZINC3873853	0.694	425.2 Da LogP -1.64 TPSA 223.4	2 viol.	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@@H](CO[P@](=O)(O)CP(=O…`
ZINC3873854	0.694	425.2 Da LogP -1.64 TPSA 223.4	2 viol.	✓ Clean	`Nc1ncnc2c1ncn2[C@H]1O[C@@H](CO[P@](=O)(O)CP(=O)…`
ZINC3873855	0.694	425.2 Da LogP -1.64 TPSA 223.4	2 viol.	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@@H](CO[P@](=O)(O)CP(=O…`
ZINC5615251	0.677	375.3 Da LogP -0.55 TPSA 164.1	1 viol.	✓ Clean	`COP(=O)(OC)OC[C@H]1O[C@@H](n2cnc3c(N)ncnc32)[C@…`
ZINC5615253	0.677	375.3 Da LogP -0.55 TPSA 164.1	1 viol.	✓ Clean	`COP(=O)(OC)OC[C@@H]1O[C@@H](n2cnc3c(N)ncnc32)[C…`
ZINC5615258	0.677	375.3 Da LogP -0.55 TPSA 164.1	1 viol.	✓ Clean	`COP(=O)(OC)OC[C@H]1O[C@@H](n2cnc3c(N)ncnc32)[C@…`
ZINC5615263	0.677	375.3 Da LogP -0.55 TPSA 164.1	1 viol.	✓ Clean	`COP(=O)(OC)OC[C@@H]1O[C@@H](n2cnc3c(N)ncnc32)[C…`
ZINC31516918	0.672	446.4 Da LogP -1.33 TPSA 218.2	1 viol.	✓ Clean	`CC(C)[C@H](N)C(=O)O[P@](=O)(O)OC[C@H]1O[C@@H](n…`
ZINC1582675	0.667	403.3 Da LogP 0.23 TPSA 164.1	1 viol.	✓ Clean	`CCOP(=O)(OCC)OC[C@H]1O[C@@H](n2cnc3c(N)ncnc32)[…`
ZINC5486730	0.667	403.3 Da LogP 0.23 TPSA 164.1	1 viol.	✓ Clean	`CCOP(=O)(OCC)OC[C@H]1O[C@@H](n2cnc3c(N)ncnc32)[…`

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.