Protein profile

KP13_00870

GMP synthase

Genome: KpKP13

Gene: AHE43233.1 guaA Structure source: AlphaFold + ColabFold UniProt A0A0H3GRL9

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Amino acids 525

Annotations 5

Features 41

PDB binders 3

Druggability 0.019

Overview

Basic information about this protein and its source genome.

Accession: KP13_00870
Assembly: Klebsiella pneumoniae subsp. pneumoniae Kp13, complete sequence
Gene: AHE43233.1 guaA
Status: annotated
Amino acids: 525
Structure source: AlphaFold + ColabFold

GO:0006164 The chemical reactions and pathways resulting in the formation of a purine nucleotide, a compound consisting of nucleoside (a purine base linked to a deoxyribose or ribose sugar) esterified with a phosphate group at either the 3' or 5'-hydroxyl group of the sugar. GO:0003922 Catalysis of the reaction: ATP + XMP + L-glutamine + H2O = AMP + diphosphate + GMP + L-glutamate + 2H+. GO:0005524 Binding to ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator. GO:0006177 The chemical reactions and pathways resulting in the formation of GMP, guanosine monophosphate. GO:0003921 Catalysis of the reaction: ATP + XMP + NH4+ = AMP + diphosphate + GMP + 2H+.

Target profile

Computed evidence for target prioritization.

Human off-target: hit
Human identity (%): 36.477
Human E-value: 2.23e-93
Gut microbiome off-target: hit
Essential (DEG): Y
DEG identity (%): 96.19
DEG E-value: 0.0
Localization: Cytoplasmic
ColabFold pLDDT: 91.84

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 0.019

Structure A0A0H3GRL9

Pocket Pocket 25

P2Rank 0.918

Structure A0A0H3GRL9

Pocket Pocket 1

ColabFold model

FPocket 0.445 · Pocket 3

P2Rank 0.901 · Pocket 1

Core conservation Conserved core gene

Roary core

CoreCruncher core

Gut microbiome 2241 / 4744 genomes with a hit

Normalized 0.472

Sequence

Primary amino-acid sequence viewer.

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

5 GO

Gene Ontology (GO)

GO:0006164 The chemical reactions and pathways resulting in the formation of a purine nucleotide, a compound consisting of nucleoside (a purine base linked to a deoxyribose or ribose sugar) esterified with a phosphate group at either the 3' or 5'-hydroxyl group of the sugar.
GO:0003922 Catalysis of the reaction: ATP + XMP + L-glutamine + H2O = AMP + diphosphate + GMP + L-glutamate + 2H+.
GO:0005524 Binding to ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
GO:0006177 The chemical reactions and pathways resulting in the formation of GMP, guanosine monophosphate.
GO:0003921 Catalysis of the reaction: ATP + XMP + NH4+ = AMP + diphosphate + GMP + 2H+.

Sequence Features

Domain/signature hits from InterPro and related databases.

41 records

Show feature table

Start	End	DB	Term	Name
208	400	ProSiteProfiles	PS51553	GMP synthetase ATP pyrophosphatase (GMPS ATP-PPase) domain profile.
208	400	InterPro	IPR025777	GMP synthetase ATP pyrophosphatase domain
433	524	Pfam	PF00958	GMP synthase C terminal domain
433	524	InterPro	IPR001674	GMP synthase, C-terminal
209	410	FunFam	G3DSA:3.40.50.620:FF:000001	GMP synthase [glutamine-hydrolyzing]
197	420	SUPERFAMILY	SSF52402	Adenine nucleotide alpha hydrolases-like
405	525	SUPERFAMILY	SSF54810	GMP synthetase C-terminal dimerisation domain
5	204	SUPERFAMILY	SSF52317	Class I glutamine amidotransferase-like
5	204	InterPro	IPR029062	Class I glutamine amidotransferase-like
10	198	CDD	cd01742	GATase1_GMP_Synthase
10	198	InterPro	IPR004739	GMP synthase, glutamine amidotransferase
10	205	NCBIfam	TIGR00888	glutamine-hydrolyzing GMP synthase, N-terminal domain
10	205	InterPro	IPR004739	GMP synthase, glutamine amidotransferase
217	258	Pfam	PF02540	NAD synthase
217	258	InterPro	IPR022310	NAD/GMP synthase
9	206	Gene3D	G3DSA:3.40.50.880	-
9	206	InterPro	IPR029062	Class I glutamine amidotransferase-like
12	199	Pfam	PF00117	Glutamine amidotransferase class-I
12	199	InterPro	IPR017926	Glutamine amidotransferase
411	525	Gene3D	G3DSA:3.30.300.10	-
229	524	CDD	cd01997	GMP_synthase_C
229	524	InterPro	IPR001674	GMP synthase, C-terminal
177	190	PRINTS	PR00096	Glutamine amidotransferase superfamily signature
54	63	PRINTS	PR00096	Glutamine amidotransferase superfamily signature
81	92	PRINTS	PR00096	Glutamine amidotransferase superfamily signature
209	410	Gene3D	G3DSA:3.40.50.620	HUPs
209	410	InterPro	IPR014729	Rossmann-like alpha/beta/alpha sandwich fold
7	525	Hamap	MF_00344	GMP synthase [glutamine-hydrolyzing] [guaA].
7	525	InterPro	IPR022955	GMP synthase
411	525	FunFam	G3DSA:3.30.300.10:FF:000002	GMP synthase [glutamine-hydrolyzing]
51	65	PRINTS	PR00099	Carbamoyl-phosphate synthase protein GATase domain signature
10	24	PRINTS	PR00099	Carbamoyl-phosphate synthase protein GATase domain signature
81	97	PRINTS	PR00099	Carbamoyl-phosphate synthase protein GATase domain signature
7	206	FunFam	G3DSA:3.40.50.880:FF:000001	GMP synthase [glutamine-hydrolyzing]
9	207	ProSiteProfiles	PS51273	Glutamine amidotransferase type 1 domain profile.
81	92	PRINTS	PR00097	Anthranilate synthase component II signature
54	63	PRINTS	PR00097	Anthranilate synthase component II signature
177	190	PRINTS	PR00097	Anthranilate synthase component II signature
10	525	PANTHER	PTHR11922	GMP SYNTHASE-RELATED
212	525	NCBIfam	TIGR00884	glutamine-hydrolyzing GMP synthase, C-terminal domain
212	525	InterPro	IPR001674	GMP synthase, C-terminal

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_A0A0H3GRL9	AlphaFold	—	—	full sequence	—	Viewing
ColabFold KP13_00870	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	17.24	0.799
2	3.16	0.107
3	3.1	0.104
4	2.06	0.046
5	1.78	0.033

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
3				0.445
5				0.319

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	20.05	0.849
2	3.36	0.12
3	2.71	0.081
4	2.44	0.066
5	2.03	0.044

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.

53 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
MLA	6JP9	Q58531	104.1 Da LogP -0.45 TPSA 74.6	✓ Ro5	✓ Clean	`C(C(=O)O)C(=O)O`
POP	1GPM	P04079	176.0 Da LogP -2.08 TPSA 129.9	✓ Ro5	✓ Clean	`O[P@@](=O)([O-])O[P@@](=O)(O)[O-]`
XMP	2VXO	P49915	365.2 Da LogP -3.44 TPSA 201.2	1 viol.	✓ Clean	`c1[nH+]c2c(n1[C@H]3[C@@H]([C@@H]([C@H](O3)COP(=…`

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
ZINC1532902	0.700	206.2 Da LogP -0.86 TPSA 132.1	✓ Ro5	✓ Clean	`O=C(O)CC[C@@](O)(CC(=O)O)C(=O)O`
ZINC2018106	0.700	206.2 Da LogP -0.86 TPSA 132.1	✓ Ro5	✓ Clean	`O=C(O)CC[C@](O)(CC(=O)O)C(=O)O`
ZINC1532710	0.661	364.2 Da LogP -2.86 TPSA 200.0	1 viol.	✓ Clean	`O=c1[nH]c(=O)c2ncn([C@H]3O[C@@H](COP(=O)(O)O)[C…`
ZINC4228292	0.661	364.2 Da LogP -2.86 TPSA 200.0	1 viol.	✓ Clean	`O=c1[nH]c(=O)c2ncn([C@@H]3O[C@H](COP(=O)(O)O)[C…`
ZINC2390999	0.655	275.3 Da LogP -1.99 TPSA 172.8	✓ Ro5	✓ Clean	`NC(=O)CC[C@H](NC(=O)CC[C@H](N)C(=O)O)C(=O)O`
ZINC3593496	0.652	206.2 Da LogP -1.16 TPSA 121.1	✓ Ro5	✓ Clean	`COC(=O)C[C@@](O)(CC(=O)O)C(=O)O`
ZINC3593497	0.652	206.2 Da LogP -1.16 TPSA 121.1	✓ Ro5	✓ Clean	`COC(=O)C[C@](O)(CC(=O)O)C(=O)O`
ZINC14686440	0.625	436.4 Da LogP -2.64 TPSA 247.9	1 viol.	✓ Clean	`O=C(O)C[C@](O)(CC(=O)NCCCCNC(=O)C[C@@](O)(CC(=O…`
ZINC14686442	0.625	436.4 Da LogP -2.64 TPSA 247.9	1 viol.	✓ Clean	`O=C(O)C[C@@](O)(CC(=O)NCCCCNC(=O)C[C@](O)(CC(=O…`
ZINC14686444	0.625	436.4 Da LogP -2.64 TPSA 247.9	1 viol.	✓ Clean	`O=C(O)C[C@@](O)(CC(=O)NCCCCNC(=O)C[C@@](O)(CC(=…`
ZINC3055005	0.591	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	0.591	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	0.591	204.2 Da LogP -0.63 TPSA 126.6	✓ Ro5	✓ Clean	`N[C@H](CCCC[C@@H](N)C(=O)O)C(=O)O`
ZINC2391099	0.586	274.3 Da LogP -2.59 TPSA 178.6	✓ Ro5	✓ Clean	`NC(=O)CC[C@H](N)C(=O)N[C@@H](CCC(N)=O)C(=O)O`
ZINC13398039	0.577	234.2 Da LogP -0.38 TPSA 121.1	✓ Ro5	✓ Clean	`CC(C)OC(=O)C[C@](O)(CC(=O)O)C(=O)O`
ZINC2528012	0.577	234.2 Da LogP -0.38 TPSA 121.1	✓ Ro5	✓ Clean	`CC(C)OC(=O)C[C@@](O)(CC(=O)O)C(=O)O`
ZINC2556600	0.567	217.2 Da LogP -1.83 TPSA 135.5	✓ Ro5	✓ Clean	`C[C@H](NC(=O)[C@@H](N)CCC(N)=O)C(=O)O`
ZINC1555366	0.565	232.3 Da LogP 0.15 TPSA 126.6	✓ Ro5	✓ Clean	`N[C@@H](CCCCCC[C@H](N)C(=O)O)C(=O)O`
ZINC1555367	0.565	232.3 Da LogP 0.15 TPSA 126.6	✓ Ro5	✓ Clean	`N[C@@H](CCCCCC[C@@H](N)C(=O)O)C(=O)O`
ZINC1555369	0.565	232.3 Da LogP 0.15 TPSA 126.6	✓ Ro5	✓ Clean	`N[C@H](CCCCCC[C@@H](N)C(=O)O)C(=O)O`
ZINC1720127	0.565	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	0.565	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	0.565	218.3 Da LogP -0.24 TPSA 126.6	✓ Ro5	✓ Clean	`N[C@H](CCCCC[C@@H](N)C(=O)O)C(=O)O`
ZINC13515793	0.561	338.2 Da LogP -2.43 TPSA 171.3	✓ Ro5	✓ Clean	`Cc1cn([C@@H]2O[C@H](COP(=O)(O)O)[C@@H](O)[C@H]2…`
ZINC13518175	0.561	450.1 Da LogP -2.13 TPSA 171.3	✓ Ro5	✓ Clean	`O=c1[nH]c(=O)n([C@@H]2O[C@H](COP(=O)(O)O)[C@@H]…`
ZINC146315135	0.560	204.2 Da LogP 0.86 TPSA 94.8	✓ Ro5	✓ Clean	`CCCCC[C@@](O)(CC(=O)O)C(=O)O`
ZINC146315336	0.560	204.2 Da LogP 0.86 TPSA 94.8	✓ Ro5	✓ Clean	`CCCCC[C@](O)(CC(=O)O)C(=O)O`
ZINC1850353	0.556	206.1 Da LogP -0.86 TPSA 132.1	✓ Ro5	✓ Clean	`O=C(O)CC(O)(CC(=O)O)CC(=O)O`
ZINC12503831	0.554	324.2 Da LogP -2.73 TPSA 171.3	✓ Ro5	✓ Clean	`O=c1ccn([C@H]2O[C@H](COP(=O)(O)O)[C@H](O)[C@H]2…`
ZINC12503833	0.554	324.2 Da LogP -2.73 TPSA 171.3	✓ Ro5	✓ Clean	`O=c1ccn([C@H]2O[C@H](COP(=O)(O)O)[C@H](O)[C@@H]…`
ZINC13512000	0.554	324.2 Da LogP -2.73 TPSA 171.3	✓ Ro5	✓ Clean	`O=c1ccn([C@@H]2O[C@H](COP(=O)(O)O)[C@H](O)[C@H]…`
ZINC1532538	0.554	324.2 Da LogP -2.73 TPSA 171.3	✓ Ro5	✓ Clean	`O=c1ccn([C@H]2O[C@@H](COP(=O)(O)O)[C@H](O)[C@@H…`
ZINC2026984	0.554	324.2 Da LogP -2.73 TPSA 171.3	✓ Ro5	✓ Clean	`O=c1ccn([C@H]2O[C@@H](COP(=O)(O)O)[C@H](O)[C@H]…`
ZINC2123545	0.554	324.2 Da LogP -2.73 TPSA 171.3	✓ Ro5	✓ Clean	`O=c1ccn([C@@H]2O[C@H](COP(=O)(O)O)[C@@H](O)[C@H…`
ZINC2606131	0.554	324.2 Da LogP -2.73 TPSA 171.3	✓ Ro5	✓ Clean	`O=c1ccn([C@@H]2O[C@H](COP(=O)(O)O)[C@@H](O)[C@@…`
ZINC36377965	0.554	324.2 Da LogP -2.73 TPSA 171.3	✓ Ro5	✓ Clean	`O=c1ccn([C@@H]2O[C@H](COP(=O)(O)O)[C@H](O)[C@@H…`
ZINC3870257	0.554	324.2 Da LogP -2.73 TPSA 171.3	✓ Ro5	✓ Clean	`O=c1ccn([C@H]2O[C@@H](COP(=O)(O)O)[C@@H](O)[C@H…`
ZINC3870258	0.554	324.2 Da LogP -2.73 TPSA 171.3	✓ Ro5	✓ Clean	`O=c1ccn([C@@H]2O[C@@H](COP(=O)(O)O)[C@@H](O)[C@…`
ZINC3870259	0.554	324.2 Da LogP -2.73 TPSA 171.3	✓ Ro5	✓ Clean	`O=c1ccn([C@H]2O[C@@H](COP(=O)(O)O)[C@@H](O)[C@@…`
ZINC3870260	0.554	324.2 Da LogP -2.73 TPSA 171.3	✓ Ro5	✓ Clean	`O=c1ccn([C@@H]2O[C@@H](COP(=O)(O)O)[C@@H](O)[C@…`
ZINC9235501	0.554	324.2 Da LogP -2.73 TPSA 171.3	✓ Ro5	✓ Clean	`O=c1ccn([C@@H]2O[C@@H](COP(=O)(O)O)[C@H](O)[C@H…`
ZINC1581634	0.552	203.2 Da LogP -2.22 TPSA 135.5	✓ Ro5	✓ Clean	`NC(=O)CC[C@H](N)C(=O)NCC(=O)O`
ZINC5500823	0.552	203.2 Da LogP -2.22 TPSA 135.5	✓ Ro5	✓ Clean	`NC(=O)CC[C@@H](N)C(=O)NCC(=O)O`
ZINC13517211	0.534	340.2 Da LogP -1.37 TPSA 154.2	✓ Ro5	✓ Clean	`O=c1ccn([C@@H]2O[C@H](COP(=O)(O)O)[C@@H](O)[C@H…`
ZINC9659886	0.532	363.2 Da LogP -2.74 TPSA 206.8	1 viol.	✓ Clean	`N=c1[nH]c(=O)c2ncn([C@@H]3O[C@@H](COP(=O)(O)O)[…`
ZINC2560992	0.531	275.3 Da LogP -1.99 TPSA 172.8	✓ Ro5	✓ Clean	`NC(=O)CC[C@H](N)C(=O)N[C@@H](CCC(=O)O)C(=O)O`
ZINC205346095	0.525	369.2 Da LogP -2.83 TPSA 214.4	✓ Ro5	✓ Clean	`O=c1[nH]c(=O)n([C@@H]2O[C@H](COP(=O)(O)O)[C@@H]…`
ZINC13398014	0.522	220.2 Da LogP -1.07 TPSA 110.1	✓ Ro5	✓ Clean	`COC(=O)CC(O)(CC(=O)OC)C(=O)O`
ZINC3861629	0.522	206.1 Da LogP -1.16 TPSA 121.1	✓ Ro5	✓ Clean	`COC(=O)C(O)(CC(=O)O)CC(=O)O`
ZINC2108714	0.519	217.3 Da LogP 1.21 TPSA 100.6	✓ Ro5	✓ Clean	`N[C@H](CCCCCCCC(=O)O)C(=O)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.