Protein profile

KP13_03902

Gamma-glutamylputrescine synthetase

Genome: KpKP13

Gene: AHE45352.1 puuA Structure source: AlphaFold + ColabFold UniProt A0A0H3GV91

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Amino acids 473

Annotations 6

Features 19

PDB binders 9

Druggability 0.115

Overview

Basic information about this protein and its source genome.

Accession: KP13_03902
Assembly: Klebsiella pneumoniae subsp. pneumoniae Kp13, complete sequence
Gene: AHE45352.1 puuA
Status: annotated
Amino acids: 473
Structure source: AlphaFold + ColabFold

GO:0004356 Catalysis of the reaction: ATP + L-glutamate + NH4+ = ADP + H+ + L-glutamine + phosphate. GO:0003824 Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic. GO:0006807 OBSOLETE. The chemical reactions and pathways involving organic or inorganic compounds that contain nitrogen. GO:0006542 OBSOLETE. The chemical reactions and pathways resulting in the formation of glutamine, 2-amino-4-carbamoylbutanoic acid. GO:0005524 Binding to ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator. GO:0006598 The chemical reactions and pathways resulting in the breakdown of polyamines, any organic compound containing two or more amino groups.

Target profile

Computed evidence for target prioritization.

Human off-target: hit
Human identity (%): 25.682
Human E-value: 2.51e-20
Gut microbiome off-target: hit
Essential (DEG): N
DEG identity (%): 0.0
Localization: Cytoplasmic
ColabFold pLDDT: 91.65

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 0.115

Structure A0A0H3GV91

Pocket Pocket 6

P2Rank 0.682

Structure A0A0H3GV91

Pocket Pocket 1

ColabFold model

FPocket 0.249 · Pocket 18

P2Rank 0.776 · Pocket 1

Core conservation Conserved core gene

Roary core

CoreCruncher core

Gut microbiome 50 / 4744 genomes with a hit

Normalized 0.011

Sequence

Primary amino-acid sequence viewer.

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

6 GO

Gene Ontology (GO)

GO:0004356 Catalysis of the reaction: ATP + L-glutamate + NH4+ = ADP + H+ + L-glutamine + phosphate.
GO:0003824 Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
GO:0006807 OBSOLETE. The chemical reactions and pathways involving organic or inorganic compounds that contain nitrogen.
GO:0006542 OBSOLETE. The chemical reactions and pathways resulting in the formation of glutamine, 2-amino-4-carbamoylbutanoic acid.
GO:0005524 Binding to ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
GO:0006598 The chemical reactions and pathways resulting in the breakdown of polyamines, any organic compound containing two or more amino groups.

Sequence Features

Domain/signature hits from InterPro and related databases.

19 records

Show feature table

Start	End	DB	Term	Name
25	132	SUPERFAMILY	SSF54368	Glutamine synthetase, N-terminal domain
25	132	InterPro	IPR036651	Glutamine synthetase, N-terminal domain superfamily
136	472	FunFam	G3DSA:3.30.590.10:FF:000008	Gamma-glutamylputrescine synthetase PuuA
134	470	SUPERFAMILY	SSF55931	Glutamine synthetase/guanido kinase
134	470	InterPro	IPR014746	Glutamine synthetase/guanido kinase, catalytic domain
134	468	Pfam	PF00120	Glutamine synthetase, catalytic domain
134	468	InterPro	IPR008146	Glutamine synthetase, catalytic domain
136	472	Gene3D	G3DSA:3.30.590.10	Glutamine synthetase/guanido kinase, catalytic domain
136	473	ProSiteProfiles	PS51987	Glutamine synthetase (GS) catalytic domain profile.
136	473	InterPro	IPR008146	Glutamine synthetase, catalytic domain
271	286	ProSitePatterns	PS00181	Glutamine synthetase putative ATP-binding region signature.
271	286	InterPro	IPR027303	Glutamine synthetase, glycine-rich site
133	390	SMART	SM01230	Gln_synt_C_2
133	390	InterPro	IPR008146	Glutamine synthetase, catalytic domain
32	129	Gene3D	G3DSA:3.10.20.70	-
32	129	InterPro	IPR036651	Glutamine synthetase, N-terminal domain superfamily
35	129	ProSiteProfiles	PS51986	Glutamine synthetase (GS) beta-grasp domain profile.
35	129	InterPro	IPR008147	Glutamine synthetase, N-terminal domain
21	471	PANTHER	PTHR43785	GAMMA-GLUTAMYLPUTRESCINE SYNTHETASE

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_A0A0H3GV91	AlphaFold	—	—	full sequence	—	Viewing
ColabFold KP13_03902	ColabFold	—	—	full sequence	—	Loaded

Pocket details FPocket · P2Rank — toggle visibility and zoom from here, or open full viewer

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	9.18	0.491
2	4.87	0.218
3	2.98	0.097
4	1.0	0.006

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
18				0.249

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	12.7	0.659
2	2.47	0.068
3	2.29	0.058
4	2.15	0.05
5	1.09	0.007

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.

59 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
1AZ	2WGS	P9WN39	424.3 Da LogP 1.63 TPSA 74.3	✓ Ro5	✓ Clean	`Cn1c2c(nc1N3CCOCC3)N(C(=O)N(C2=O)Cc4ccc(c(c4)Cl…`
2K9	4XYC	P9WN38	297.3 Da LogP 2.28 TPSA 47.3	✓ Ro5	✓ Clean	`c1ccc(cc1)c2cccc3c2C=C4C3=NC(=O)c5n4ccn5`
46B	4ACF	P9WN39	418.3 Da LogP 4.44 TPSA 75.9	✓ Ro5	✓ Clean	`CCCCNc1c(nc2n1cc(cc2)Br)c3ccc(cc3)OCC(=O)O`
ANP	3NG0	P77961	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)…`
IQ1	3ZXR	P9WN39	328.4 Da LogP 4.98 TPSA 54.5	✓ Ro5	✓ Clean	`CC(C)(C)c1[nH]c(c(n1)c2cc3ccccc3nc2)c4ccncc4`
MXI	3ZXV	P9WN39	372.5 Da LogP 5.18 TPSA 76.8	1 viol.	✓ Clean	`CC(C)(C)c1[nH]c(c(n1)c2ccc3cc(ccc3c2)OC)c4ccnc(…`
P3P	5ZLP	P94845	261.1 Da LogP -0.19 TPSA 147.2	✓ Ro5	✓ Clean	`C[P@](=O)(CC[C@@H](C(=O)O)N)OP(=O)(O)O`
P3S	4LNI	P12425	260.2 Da LogP -1.02 TPSA 150.3	✓ Ro5	✓ Clean	`C[S@](=NP(=O)(O)O)(=O)CC[C@@H](C(=O)O)N`
PPQ	5ZLP	P94845	181.1 Da LogP -0.31 TPSA 100.6	✓ Ro5	✓ Clean	`C[P@](=O)(CC[C@@H](C(=O)O)N)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
ZINC1094334	0.843	389.8 Da LogP 0.97 TPSA 74.3	✓ Ro5	✓ Clean	`Cn1c(N2CCOCC2)nc2c1c(=O)n(Cc1ccc(Cl)cc1)c(=O)n2C`
ZINC8916385	0.827	422.3 Da LogP 2.78 TPSA 65.1	✓ Ro5	✓ Clean	`Cn1c(N2CCCCC2)nc2c1c(=O)n(Cc1ccc(Cl)c(Cl)c1)c(=…`
ZINC1094329	0.811	436.3 Da LogP 3.03 TPSA 65.1	✓ Ro5	✓ Clean	`CC1CCN(c2nc3c(c(=O)n(Cc4ccc(Cl)c(Cl)c4)c(=O)n3C…`
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(=…`
ZINC7425789	0.808	369.4 Da LogP 0.63 TPSA 74.3	✓ Ro5	✓ Clean	`Cc1ccc(Cn2c(=O)c3c(nc(N4CCOCC4)n3C)n(C)c2=O)cc1`
ZINC13388673	0.804	355.4 Da LogP 0.32 TPSA 74.3	✓ Ro5	✓ Clean	`Cn1c(N2CCOCC2)nc2c1c(=O)n(Cc1ccccc1)c(=O)n2C`
ZINC1127306	0.792	373.4 Da LogP 0.46 TPSA 74.3	✓ Ro5	✓ Clean	`Cn1c(N2CCOCC2)nc2c1c(=O)n(Cc1ccc(F)cc1)c(=O)n2C`
ZINC6444971	0.792	434.3 Da LogP 1.08 TPSA 74.3	✓ Ro5	✓ Clean	`Cn1c(N2CCOCC2)nc2c1c(=O)n(Cc1ccc(Br)cc1)c(=O)n2C`
ZINC8926317	0.792	424.3 Da LogP 1.63 TPSA 74.3	✓ Ro5	✓ Clean	`Cn1c(=O)c2c(nc(N3CCOCC3)n2Cc2ccc(Cl)c(Cl)c2)n(C…`
ZINC13115750	0.750	452.3 Da LogP 2.40 TPSA 74.3	✓ Ro5	✓ Clean	`C[C@H]1CN(c2nc3c(c(=O)n(Cc4ccc(Cl)c(Cl)c4)c(=O)…`
ZINC2265176	0.750	452.3 Da LogP 2.40 TPSA 74.3	✓ Ro5	✓ Clean	`C[C@@H]1CN(c2nc3c(c(=O)n(Cc4ccc(Cl)c(Cl)c4)c(=O…`
ZINC38154058	0.750	452.3 Da LogP 2.40 TPSA 74.3	✓ Ro5	✓ Clean	`C[C@H]1CN(c2nc3c(c(=O)n(Cc4ccc(Cl)c(Cl)c4)c(=O)…`
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…`
ZINC9324586	0.741	465.3 Da LogP 1.49 TPSA 108.2	✓ Ro5	✓ Clean	`Cn1c(N2CCC(C(N)=O)CC2)nc2c1c(=O)n(Cc1ccc(Cl)c(C…`
ZINC1127852	0.737	424.3 Da LogP 1.63 TPSA 74.3	✓ Ro5	✓ Clean	`Cn1c(N2CCOCC2)nc2c1c(=O)n(Cc1ccc(Cl)cc1Cl)c(=O)…`
ZINC1133233	0.736	431.5 Da LogP 1.83 TPSA 74.3	✓ Ro5	✓ Clean	`Cn1c(=O)n(Cc2ccccc2)c(=O)c2c1nc(N1CCOCC1)n2Cc1c…`
ZINC1277814	0.732	389.8 Da LogP 0.97 TPSA 74.3	✓ Ro5	✓ Clean	`Cn1c(N2CCOCC2)nc2c1c(=O)n(Cc1ccccc1Cl)c(=O)n2C`
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)…`
ZINC23115420	0.702	383.5 Da LogP 1.36 TPSA 74.3	✓ Ro5	✓ Clean	`CC(C)n1c(N2CCOCC2)nc2c1c(=O)n(Cc1ccccc1)c(=O)n2C`

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.