Protein profile

KP13_02386

GTP pyrophosphokinase

Genome: KpKP13

Gene: AHE42957.1 relA Structure source: AlphaFold + ColabFold UniProt A0A0H3GXH6

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Amino acids 745

Annotations 10

Features 42

PDB binders 3

Druggability 0.911

Overview

Basic information about this protein and its source genome.

Accession: KP13_02386
Assembly: Klebsiella pneumoniae subsp. pneumoniae Kp13, complete sequence
Gene: AHE42957.1 relA
Status: annotated
Amino acids: 745
Structure source: AlphaFold + ColabFold

2.7.6.5

GO:0015969 The chemical reactions and pathways involving guanine tetraphosphate (5'-ppGpp-3'), a derivative of guanine riboside with four phosphates. GO:0005886 The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins. GO:0005524 Binding to ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator. GO:0005525 Binding to GTP, guanosine triphosphate. GO:0008728 Catalysis of the reaction: ATP + GTP = AMP + guanosine 3'-diphosphate 5'-triphosphate. GO:0008893 Catalysis of the reaction: guanosine 3',5'-bis(diphosphate) + H2O = diphosphate + GDP + H+.

Target profile

Computed evidence for target prioritization.

Human off-target: No hit
Human identity (%): 0.0
Gut microbiome off-target: hit
Essential (DEG): Y
DEG identity (%): 66.353
DEG E-value: 0.0
Localization: Cytoplasmic
ColabFold pLDDT: 79.45

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 0.911

Structure A0A0H3GXH6

Pocket Pocket 1

P2Rank 0.753

Structure A0A0H3GXH6

Pocket Pocket 1

ColabFold model

FPocket 0.394 · Pocket 20

P2Rank 0.768 · Pocket 1

Core conservation Conserved core gene

Roary core

CoreCruncher core

Gut microbiome 153 / 4744 genomes with a hit

Normalized 0.032

Sequence

Primary amino-acid sequence viewer.

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 9 GO

Enzyme Commission (EC)

2.7.6.5

Gene Ontology (GO)

GO:0015969 The chemical reactions and pathways involving guanine tetraphosphate (5'-ppGpp-3'), a derivative of guanine riboside with four phosphates.
GO:0005886 The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.
GO:0005524 Binding to ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
GO:0005525 Binding to GTP, guanosine triphosphate.
GO:0008728 Catalysis of the reaction: ATP + GTP = AMP + guanosine 3'-diphosphate 5'-triphosphate.
GO:0008893 Catalysis of the reaction: guanosine 3',5'-bis(diphosphate) + H2O = diphosphate + GDP + H+.
GO:0016301 Catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule.
GO:0015949 The chemical reactions and pathways by which a nucleobase, nucleoside or nucleotide small molecule is synthesized from another nucleobase, nucleoside or nucleotide small molecule.
GO:0042594 Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a starvation stimulus, deprivation of nourishment.

Sequence Features

Domain/signature hits from InterPro and related databases.

42 records

Show feature table

Start	End	DB	Term	Name
196	411	SUPERFAMILY	SSF81301	Nucleotidyltransferase
196	411	InterPro	IPR043519	Nucleotidyltransferase superfamily
670	741	CDD	cd04876	ACT_RelA-SpoT
208	341	Gene3D	G3DSA:3.30.460.10	Beta Polymerase, domain 2
208	341	InterPro	IPR043519	Nucleotidyltransferase superfamily
401	474	Gene3D	G3DSA:3.10.20.30	-
401	474	InterPro	IPR012675	Beta-grasp domain superfamily
405	466	ProSiteProfiles	PS51880	TGS domain profile.
405	466	InterPro	IPR004095	TGS
52	741	PANTHER	PTHR21262	GUANOSINE-3',5'-BIS DIPHOSPHATE 3'-PYROPHOSPHOHYDROLASE
208	341	FunFam	G3DSA:3.30.460.10:FF:000001	GTP pyrophosphokinase RelA
665	741	Pfam	PF13291	ACT domain
665	741	InterPro	IPR002912	ACT domain
400	473	FunFam	G3DSA:3.10.20.30:FF:000002	GTP pyrophosphokinase (RelA/SpoT)
27	207	Gene3D	G3DSA:1.10.3210.10	Hypothetical protein af1432
484	647	Pfam	PF19296	RelA/SpoT, AH and RIS domains
484	647	InterPro	IPR045600	RelA/SpoT, AH and RIS domains
227	349	CDD	cd05399	NT_Rel-Spo_like
227	349	InterPro	IPR007685	RelA/SpoT
408	466	CDD	cd01668	TGS_RSH
408	466	InterPro	IPR033655	RelA/SpoT, TGS domain
665	744	Gene3D	G3DSA:3.30.70.260	-
251	360	Pfam	PF04607	Region found in RelA / SpoT proteins
251	360	InterPro	IPR007685	RelA/SpoT
55	160	ProSiteProfiles	PS51831	HD domain profile.
55	160	InterPro	IPR006674	HD domain
48	191	Pfam	PF13328	HD domain
24	207	SUPERFAMILY	SSF109604	HD-domain/PDEase-like
36	207	FunFam	G3DSA:1.10.3210.10:FF:000007	GTP pyrophosphokinase
407	466	Pfam	PF02824	TGS domain
407	466	InterPro	IPR004095	TGS
251	361	SMART	SM00954	RelA_SpoT_2
251	361	InterPro	IPR007685	RelA/SpoT
666	742	SUPERFAMILY	SSF55021	ACT-like
666	742	InterPro	IPR045865	ACT-like domain
400	466	SUPERFAMILY	SSF81271	TGS-like
400	466	InterPro	IPR012676	TGS-like
63	740	NCBIfam	TIGR00691	RelA/SpoT family protein
63	740	InterPro	IPR004811	RelA/SpoT family
669	744	ProSiteProfiles	PS51671	ACT domain profile.
669	744	InterPro	IPR002912	ACT domain
665	744	FunFam	G3DSA:3.30.70.260:FF:000010	GTP pyrophosphokinase RelA

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_A0A0H3GXH6	AlphaFold	—	—	full sequence	—	Viewing
ColabFold KP13_02386	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				0.911
59				0.852

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	11.76	0.624
2	9.49	0.51
3	4.7	0.206
4	4.18	0.17
5	1.95	0.041

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
20				0.394

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	11.9	0.63
2	3.21	0.111
3	3.09	0.103
4	2.65	0.077
5	1.77	0.032

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.

60 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
G4P	6S2T	Q5SHL3	603.2 Da LogP -2.22 TPSA 345.6	3 viol.	✓ Clean	`c1nc2c(n1[C@H]3[C@@H]([C@@H]([C@H](O3)CO[P@](=O…`
GN3	6S2U	Q5SHL3	602.2 Da LogP -2.65 TPSA 348.4	3 viol.	✓ Clean	`c1nc2c(n1[C@H]3[C@@H]([C@@H]([C@H](O3)COP(=O)(O…`
GPX	1VJ7	Q54089	505.2 Da LogP -1.29 TPSA 267.9	3 viol.	✓ Clean	`c1nc2c(n1[C@H]3[C@H]4[C@@H]([C@H](O3)CO[P@](=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).

Ligand	UniProt (homolog)	pchembl	MW · LogP · TPSA	Lipinski	PAINS	SMILES
CHEMBL1163519	P0AG20	—	425.2 Da LogP -1.31 TPSA 223.1	1 viol.	✓ Clean	`Nc1nc2c(ncn2[C@H]2C[C@H](OP(=O)(O)CP(=O)(O)O)[C…`
CHEMBL1163520	P0AG20	—	669.3 Da LogP -0.98 TPSA 330.2	3 viol.	✓ Clean	`CC(C)C(=O)Nc1nc2c(ncn2[C@@H]2O[C@H](COP(=O)(O)C…`
CHEMBL1163568	P0AG20	—	599.2 Da LogP -2.00 TPSA 327.2	3 viol.	✓ Clean	`Nc1nc2c(ncn2[C@@H]2O[C@H](COP(=O)(O)CP(=O)(O)O)…`
CHEMBL1163576	P0AG20	—	583.2 Da LogP -0.97 TPSA 306.9	3 viol.	✓ Clean	`Nc1nc2c(ncn2[C@H]2C[C@H](OP(=O)(O)CP(=O)(O)O)[C…`
CHEMBL1163621	P0AG20	—	481.3 Da LogP -0.54 TPSA 221.3	1 viol.	✓ Clean	`CC1(C)O[C@@H]2[C@H](O1)[C@@H](COP(=O)(O)CP(=O)(…`
CHEMBL1164398	P0AG20	—	783.6 Da LogP 2.04 TPSA 319.2	3 viol.	✓ Clean	`CC(C)C(=O)Nc1nc2c(ncn2[C@@H]2O[C@H](COP(=O)(O)C…`
GP2	P0AG20	—	441.2 Da LogP -2.34 TPSA 243.3	2 viol.	✓ Clean	`c1nc2c(n1[C@H]3[C@@H]([C@@H]([C@H](O3)CO[P@](=O…`

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
ZINC14963236	0.862	347.2 Da LogP -1.54 TPSA 185.8	✓ Ro5	✓ Clean	`Nc1nc2c(ncn2[C@@H]2C[C@@H](OP(=O)(O)O)[C@@H](CO…`
ZINC14963244	0.862	347.2 Da LogP -1.54 TPSA 185.8	✓ Ro5	✓ Clean	`Nc1nc2c(ncn2[C@@H]2C[C@H](OP(=O)(O)O)[C@@H](CO)…`
ZINC14963248	0.862	347.2 Da LogP -1.54 TPSA 185.8	✓ Ro5	✓ Clean	`Nc1nc2c(ncn2[C@H]2C[C@H](OP(=O)(O)O)[C@@H](CO)O…`
ZINC2522482	0.862	347.2 Da LogP -1.54 TPSA 185.8	✓ Ro5	✓ Clean	`Nc1nc2c(ncn2[C@@H]2C[C@@H](OP(=O)(O)O)[C@H](CO)…`
ZINC4543679	0.862	347.2 Da LogP -1.54 TPSA 185.8	✓ Ro5	✓ Clean	`Nc1nc2c(ncn2[C@@H]2C[C@H](OP(=O)(O)O)[C@H](CO)O…`
ZINC4543681	0.862	347.2 Da LogP -1.54 TPSA 185.8	✓ Ro5	✓ Clean	`Nc1nc2c(ncn2[C@H]2C[C@H](OP(=O)(O)O)[C@H](CO)O2…`
ZINC4543684	0.862	347.2 Da LogP -1.54 TPSA 185.8	✓ Ro5	✓ Clean	`Nc1nc2c(ncn2[C@H]2C[C@@H](OP(=O)(O)O)[C@H](CO)O…`
ZINC13783924	0.719	323.3 Da LogP -0.89 TPSA 137.5	✓ Ro5	✓ Clean	`CC1(C)O[C@H]2[C@@H](CO)O[C@@H](n3cnc4c(=O)[nH]c…`
ZINC13783925	0.719	323.3 Da LogP -0.89 TPSA 137.5	✓ Ro5	✓ Clean	`CC1(C)O[C@@H]2[C@H](CO)O[C@@H](n3cnc4c(=O)[nH]c…`
ZINC22061608	0.719	323.3 Da LogP -0.89 TPSA 137.5	✓ Ro5	✓ Clean	`CC1(C)O[C@H]2[C@H](O1)[C@@H](CO)O[C@H]2n1cnc2c(…`
ZINC22061611	0.719	323.3 Da LogP -0.89 TPSA 137.5	✓ Ro5	✓ Clean	`CC1(C)O[C@@H]2[C@H](O1)[C@H](n1cnc3c(=O)[nH]c(N…`
ZINC402983	0.719	323.3 Da LogP -0.89 TPSA 137.5	✓ Ro5	✓ Clean	`CC1(C)O[C@H]2[C@H](CO)O[C@H](n3cnc4c(=O)[nH]c(N…`
ZINC4556553	0.719	323.3 Da LogP -0.89 TPSA 137.5	✓ Ro5	✓ Clean	`CC1(C)O[C@@H]2[C@H](CO)O[C@H](n3cnc4c(=O)[nH]c(…`
ZINC5762619	0.719	323.3 Da LogP -0.89 TPSA 137.5	✓ Ro5	✓ Clean	`CC1(C)O[C@@H]2[C@@H](CO)O[C@@H](n3cnc4c(=O)[nH]…`
ZINC12503440	0.692	363.2 Da LogP -2.57 TPSA 206.0	1 viol.	✓ Clean	`Nc1nc2c(ncn2[C@@H]2O[C@H](CO)[C@@H](OP(=O)(O)O)…`
ZINC1530370	0.692	363.2 Da LogP -2.57 TPSA 206.0	1 viol.	✓ Clean	`Nc1nc2c(ncn2[C@H]2O[C@@H](CO)[C@H](OP(=O)(O)O)[…`
ZINC28631009	0.692	363.2 Da LogP -2.57 TPSA 206.0	1 viol.	✓ Clean	`Nc1nc2c(ncn2[C@@H]2O[C@H](CO)[C@H](OP(=O)(O)O)[…`
ZINC3872740	0.692	363.2 Da LogP -2.57 TPSA 206.0	1 viol.	✓ Clean	`Nc1nc2c(ncn2[C@H]2O[C@@H](CO)[C@@H](OP(=O)(O)O)…`
ZINC3872741	0.692	363.2 Da LogP -2.57 TPSA 206.0	1 viol.	✓ Clean	`Nc1nc2c(ncn2[C@@H]2O[C@@H](CO)[C@@H](OP(=O)(O)O…`
ZINC3872742	0.692	363.2 Da LogP -2.57 TPSA 206.0	1 viol.	✓ Clean	`Nc1nc2c(ncn2[C@H]2O[C@@H](CO)[C@@H](OP(=O)(O)O)…`
ZINC3872743	0.692	363.2 Da LogP -2.57 TPSA 206.0	1 viol.	✓ Clean	`Nc1nc2c(ncn2[C@@H]2O[C@@H](CO)[C@@H](OP(=O)(O)O…`
ZINC12501413	0.688	363.2 Da LogP -2.57 TPSA 206.0	1 viol.	✓ Clean	`Nc1nc2c(ncn2[C@@H]2O[C@H](COP(=O)(O)O)[C@@H](O)…`
ZINC12958448	0.688	363.2 Da LogP -2.57 TPSA 206.0	1 viol.	✓ Clean	`Nc1nc2c(ncn2[C@@H]2O[C@H](COP(=O)(O)O)[C@H](O)[…`
ZINC1532555	0.688	363.2 Da LogP -2.57 TPSA 206.0	1 viol.	✓ Clean	`Nc1nc2c(ncn2[C@H]2O[C@@H](COP(=O)(O)O)[C@H](O)[…`
ZINC16546189	0.688	363.2 Da LogP -2.57 TPSA 206.0	1 viol.	✓ Clean	`Nc1nc2c(ncn2[C@@H]2O[C@H](COP(=O)(O)O)[C@H](O)[…`
ZINC2159505	0.688	363.2 Da LogP -2.57 TPSA 206.0	1 viol.	✓ Clean	`Nc1nc2c(ncn2[C@@H]2O[C@H](COP(=O)(O)O)[C@@H](O)…`
ZINC3073318	0.688	363.2 Da LogP -2.57 TPSA 206.0	1 viol.	✓ Clean	`Nc1nc2c(ncn2[C@H]2O[C@@H](COP(=O)(O)O)[C@@H](O)…`
ZINC3869963	0.688	363.2 Da LogP -2.57 TPSA 206.0	1 viol.	✓ Clean	`Nc1nc2c(ncn2[C@H]2O[C@@H](COP(=O)(O)O)[C@@H](O)…`
ZINC3869965	0.688	363.2 Da LogP -2.57 TPSA 206.0	1 viol.	✓ Clean	`Nc1nc2c(ncn2[C@@H]2O[C@@H](COP(=O)(O)O)[C@@H](O…`
ZINC9334496	0.688	363.2 Da LogP -2.57 TPSA 206.0	1 viol.	✓ Clean	`Nc1nc2c(ncn2[C@H]2O[C@@H](COP(=O)(O)O)[C@H](O)[…`
ZINC10512	0.683	267.2 Da LogP -1.66 TPSA 139.3	✓ Ro5	✓ Clean	`Nc1nc2c(ncn2[C@@H]2C[C@@H](O)[C@H](CO)O2)c(=O)[…`
ZINC3869839	0.683	267.2 Da LogP -1.66 TPSA 139.3	✓ Ro5	✓ Clean	`Nc1nc2c(ncn2[C@@H]2C[C@H](O)[C@H](CO)O2)c(=O)[n…`
ZINC3983944	0.683	267.2 Da LogP -1.66 TPSA 139.3	✓ Ro5	✓ Clean	`Nc1nc2c(ncn2[C@@H]2C[C@H](O)[C@@H](CO)O2)c(=O)[…`
ZINC404254	0.683	267.2 Da LogP -1.66 TPSA 139.3	✓ Ro5	✓ Clean	`Nc1nc2c(ncn2[C@H]2C[C@@H](O)[C@@H](CO)O2)c(=O)[…`
ZINC404255	0.683	267.2 Da LogP -1.66 TPSA 139.3	✓ Ro5	✓ Clean	`Nc1nc2c(ncn2[C@H]2C[C@@H](O)[C@H](CO)O2)c(=O)[n…`
ZINC404256	0.683	267.2 Da LogP -1.66 TPSA 139.3	✓ Ro5	✓ Clean	`Nc1nc2c(ncn2[C@H]2C[C@H](O)[C@@H](CO)O2)c(=O)[n…`
ZINC404257	0.683	267.2 Da LogP -1.66 TPSA 139.3	✓ Ro5	✓ Clean	`Nc1nc2c(ncn2[C@H]2C[C@H](O)[C@H](CO)O2)c(=O)[nH…`
ZINC8613543	0.683	267.2 Da LogP -1.66 TPSA 139.3	✓ Ro5	✓ Clean	`Nc1nc2c(ncn2[C@@H]2C[C@@H](O)[C@@H](CO)O2)c(=O)…`
ZINC6585348	0.672	266.3 Da LogP -1.69 TPSA 145.1	✓ Ro5	✓ Clean	`Nc1nc2c(ncn2[C@H]2C[C@H](N)[C@@H](CO)O2)c(=O)[n…`
ZINC88466058	0.667	401.4 Da LogP -0.03 TPSA 154.6	✓ Ro5	✓ Clean	`Nc1nc2c(ncn2[C@H]2C[C@H](OC(=O)COc3ccccc3)[C@@H…`
ZINC3790336	0.661	269.2 Da LogP -0.68 TPSA 119.0	✓ Ro5	✓ Clean	`Nc1nc2c(ncn2[C@H]2C[C@H](F)[C@@H](CO)O2)c(=O)[n…`
ZINC104869865	0.647	443.2 Da LogP -2.45 TPSA 252.6	2 viol.	✓ Clean	`Nc1nc2c(ncn2[C@H]2O[C@H](CO[P@@](=O)(O)OP(=O)(O…`
ZINC12504289	0.647	443.2 Da LogP -2.45 TPSA 252.6	2 viol.	✓ Clean	`Nc1nc2c(ncn2[C@@H]2O[C@H](CO[P@@](=O)(O)OP(=O)(…`
ZINC34541308	0.647	443.2 Da LogP -2.45 TPSA 252.6	2 viol.	✓ Clean	`Nc1nc2c(ncn2[C@@H]2O[C@H](CO[P@@](=O)(O)OP(=O)(…`
ZINC35000839	0.647	443.2 Da LogP -2.45 TPSA 252.6	2 viol.	✓ Clean	`Nc1nc2c(ncn2[C@H]2O[C@@H](CO[P@@](=O)(O)OP(=O)(…`
ZINC45284491	0.647	443.2 Da LogP -2.45 TPSA 252.6	2 viol.	✓ Clean	`Nc1nc2c(ncn2[C@H]2O[C@@H](CO[P@@](=O)(O)OP(=O)(…`
ZINC80639694	0.647	443.2 Da LogP -2.45 TPSA 252.6	2 viol.	✓ Clean	`Nc1nc2c(ncn2[C@@H]2O[C@H](CO[P@@](=O)(O)OP(=O)(…`
ZINC8215481	0.647	443.2 Da LogP -2.45 TPSA 252.6	2 viol.	✓ Clean	`Nc1nc2c(ncn2[C@@H]2O[C@H](CO[P@@](=O)(O)OP(=O)(…`
ZINC12296728	0.646	347.2 Da LogP -1.54 TPSA 185.8	✓ Ro5	✓ Clean	`Nc1nc2c(ncn2[C@H]2C[C@@H](O)[C@@H](COP(=O)(O)O)…`
ZINC13527603	0.646	347.2 Da LogP -1.54 TPSA 185.8	✓ Ro5	✓ Clean	`Nc1nc2c(ncn2[C@@H]2C[C@H](O)[C@@H](COP(=O)(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.