Protein profile

KP13_00164

Bifunctional (p)ppGpp synthase/hydrolase SpoT

Genome: KpKP13

Gene: spoT AHE42084.1 Structure source: AlphaFold + ColabFold UniProt A0A0H3GYT9
Amino acids 706
Annotations 8
Features 47
PDB binders 5
Druggability 0.313

Overview

Basic information about this protein and its source genome.

Accession
KP13_00164
Gene
spoT AHE42084.1
Status
annotated
Amino acids
706
Structure source
AlphaFold + ColabFold

Target profile

Computed evidence for target prioritization.

Human off-target
hit
Human identity (%)
37.778
Human E-value
6.03e-12
Gut microbiome off-target
hit
Essential (DEG)
Y
DEG identity (%)
96.317
DEG E-value
0.0
Localization
Cytoplasmic
ColabFold pLDDT
81.79

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 0.313
Structure A0A0H3GYT9
Pocket Pocket 30
P2Rank 0.896
Structure A0A0H3GYT9
Pocket Pocket 1
ColabFold model
FPocket 0.596 · Pocket 32
P2Rank 0.852 · Pocket 1
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 171 / 4744 genomes with a hit
Normalized 0.036

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)

1

Gene Ontology (GO)

7
  • 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: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:0015970 The chemical reactions and pathways resulting in the formation of guanine tetraphosphate (5'-ppGpp-3'), a derivative of guanine riboside with four phosphates.
  • 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.

47 records
Show feature table
Start End DB Term Name
192 325 FunFam G3DSA:3.30.460.10:FF:000001 GTP pyrophosphokinase RelA
626 703 Pfam PF13291 ACT domain
626 703 InterPro IPR002912 ACT domain
644 664 Coils Coil Coil
627 706 FunFam G3DSA:3.30.70.260:FF:000006 (P)ppGpp synthase/hydrolase SpoT
382 455 FunFam G3DSA:3.10.20.30:FF:000002 GTP pyrophosphokinase (RelA/SpoT)
382 456 Gene3D G3DSA:3.10.20.30 -
382 456 InterPro IPR012675 Beta-grasp domain superfamily
633 703 CDD cd04876 ACT_RelA-SpoT
627 706 Gene3D G3DSA:3.30.70.260 -
632 706 ProSiteProfiles PS51671 ACT domain profile.
632 706 InterPro IPR002912 ACT domain
26 703 NCBIfam TIGR00691 RelA/SpoT family protein
26 703 InterPro IPR004811 RelA/SpoT family
389 448 Pfam PF02824 TGS domain
389 448 InterPro IPR004095 TGS
214 333 CDD cd05399 NT_Rel-Spo_like
214 333 InterPro IPR007685 RelA/SpoT
2 191 FunFam G3DSA:1.10.3210.10:FF:000001 GTP pyrophosphokinase RelA
26 175 Pfam PF13328 HD domain
2 190 Gene3D G3DSA:1.10.3210.10 Hypothetical protein af1432
235 345 SMART SM00954 RelA_SpoT_2
235 345 InterPro IPR007685 RelA/SpoT
235 344 Pfam PF04607 Region found in RelA / SpoT proteins
235 344 InterPro IPR007685 RelA/SpoT
631 703 SUPERFAMILY SSF55021 ACT-like
631 703 InterPro IPR045865 ACT-like domain
5 703 PANTHER PTHR21262 GUANOSINE-3',5'-BIS DIPHOSPHATE 3'-PYROPHOSPHOHYDROLASE
376 448 SUPERFAMILY SSF81271 TGS-like
376 448 InterPro IPR012676 TGS-like
387 448 ProSiteProfiles PS51880 TGS domain profile.
387 448 InterPro IPR004095 TGS
41 153 SMART SM00471 hd_13
41 153 InterPro IPR003607 HD/PDEase domain
2 190 SUPERFAMILY SSF109604 HD-domain/PDEase-like
43 166 CDD cd00077 HDc
43 166 InterPro IPR003607 HD/PDEase domain
192 325 Gene3D G3DSA:3.30.460.10 Beta Polymerase, domain 2
192 325 InterPro IPR043519 Nucleotidyltransferase superfamily
390 448 CDD cd01668 TGS_RSH
390 448 InterPro IPR033655 RelA/SpoT, TGS domain
180 393 SUPERFAMILY SSF81301 Nucleotidyltransferase
180 393 InterPro IPR043519 Nucleotidyltransferase superfamily
45 144 ProSiteProfiles PS51831 HD domain profile.
45 144 InterPro IPR006674 HD domain
460 543 Pfam PF19296 RelA/SpoT, AH and RIS domains
460 543 InterPro IPR045600 RelA/SpoT, AH and RIS domains

3D Structure

Selected loaded structure. Experimental PDB entries may cover only a portion of the sequence; predicted models typically cover the full protein.

3D visualization script Full viewer

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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_A0A0H3GYT9
AlphaFold full sequence Viewing
ColabFold KP13_00164
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
30 0.313
10 0.233

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 Sticks Spheres Surfaces Score Probability Labels Zoom Positions
1 15.75 0.761
2 15.73 0.76
3 3.8 0.147
4 2.71 0.081
5 2.3 0.058

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.

62 records

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.

Show only:
Ligand Source crystal UniProt (homolog) MW · LogP · TPSA Lipinski PAINS SMILES
0O2 W8U368 683.1 Da LogP -2.10 TPSA 392.2 3 viol. ✓ Clean c1nc2c(n1[C@H]3[C@@H]([C@@H]([C@H](O3)COP(=O)(O…
APC W8U368 505.2 Da LogP -1.52 TPSA 269.9 3 viol. ✓ Clean c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)…
G4P 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 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 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)…

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.