Protein profile

KP13_01608

Phosphoribosylglycinamide formyltransferase 2

Genome: KpKP13

Gene: purT AHE43869.1 Structure source: AlphaFold + ColabFold UniProt A0A0H3GQ50
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Amino acids 392
Annotations 10
Features 21
PDB binders 8
Druggability 0.36

Overview

Basic information about this protein and its source genome.

Accession
KP13_01608
Assembly
Klebsiella pneumoniae subsp. pneumoniae Kp13, complete sequence
Gene
purT AHE43869.1
Status
annotated
Amino acids
392
Structure source
AlphaFold + ColabFold
EC
6.3.1.21
GO
GO:0009152 The chemical reactions and pathways resulting in the formation of a purine ribonucleotide, a compound consisting of ribonucleoside (a purine base linked to a ribose sugar) esterified with a phosphate group at either the 3' or 5'-hydroxyl group of the sugar. GO:0046872 Binding to a metal ion. GO:0004644 Catalysis of the reaction: 10-formyltetrahydrofolate + N1-(5-phospho-D-ribosyl)glycinamide = tetrahydrofolate + N2-formyl-N1-(5-phospho-D-ribosyl)glycinamide. GO:0000287 Binding to a magnesium (Mg) ion. GO:0016742 Catalysis of the transfer of a hydroxymethyl- or formyl group from one compound (donor) to another (acceptor). 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
No hit
Human identity (%)
0.0
Gut microbiome off-target
hit
Essential (DEG)
N
DEG identity (%)
0.0
Localization
CytoplasmicMembrane
ColabFold pLDDT
97.08

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 0.36
Structure A0A0H3GQ50
Pocket Pocket 1
P2Rank 0.967
Structure A0A0H3GQ50
Pocket Pocket 1
ColabFold model
FPocket 0.175 · Pocket 5
P2Rank 0.968 · Pocket 1
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 626 / 4744 genomes with a hit
Normalized 0.132

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)

1

Gene Ontology (GO)

9
  • GO:0009152 The chemical reactions and pathways resulting in the formation of a purine ribonucleotide, a compound consisting of ribonucleoside (a purine base linked to a ribose sugar) esterified with a phosphate group at either the 3' or 5'-hydroxyl group of the sugar.
  • GO:0046872 Binding to a metal ion.
  • GO:0004644 Catalysis of the reaction: 10-formyltetrahydrofolate + N1-(5-phospho-D-ribosyl)glycinamide = tetrahydrofolate + N2-formyl-N1-(5-phospho-D-ribosyl)glycinamide.
  • GO:0000287 Binding to a magnesium (Mg) ion.
  • GO:0016742 Catalysis of the transfer of a hydroxymethyl- or formyl group from one compound (donor) to another (acceptor).
  • 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:0043815 Catalysis of the reaction: ATP + formate + N1-(5-phospho-beta-D-ribosyl)glycinamide = ADP + H+ + N2-formyl-N1-(5-phospho-beta-D-ribosyl)glycinamide + phosphate.
  • GO:0006189 The chemical reactions and pathways resulting in the formation of IMP, inosine monophosphate, by the stepwise assembly of a purine ring on ribose 5-phosphate.

Sequence Features

Domain/signature hits from InterPro and related databases.

21 records
Show feature table
Start End DB Term Name
14 390 NCBIfam TIGR01142 phosphoribosylglycinamide formyltransferase 2
14 390 InterPro IPR005862 Formate-dependent phosphoribosylglycinamide formyltransferase
8 391 Hamap MF_01643 Formate-dependent phosphoribosylglycinamide formyltransferase [purT].
8 391 InterPro IPR005862 Formate-dependent phosphoribosylglycinamide formyltransferase
319 391 SUPERFAMILY SSF51246 Rudiment single hybrid motif
319 391 InterPro IPR011054 Rudiment single hybrid motif
197 390 FunFam G3DSA:3.30.470.20:FF:000027 Formate-dependent phosphoribosylglycinamide formyltransferase
2 123 FunFam G3DSA:3.40.50.20:FF:000007 Formate-dependent phosphoribosylglycinamide formyltransferase
119 308 ProSiteProfiles PS50975 ATP-grasp fold profile.
119 308 InterPro IPR011761 ATP-grasp fold
3 112 SUPERFAMILY SSF52440 PreATP-grasp domain
3 112 InterPro IPR016185 Pre-ATP-grasp domain superfamily
123 196 Gene3D G3DSA:3.30.1490.20 -
123 196 InterPro IPR013815 ATP-grasp fold, subdomain 1
124 196 FunFam G3DSA:3.30.1490.20:FF:000013 Formate-dependent phosphoribosylglycinamide formyltransferase
113 314 SUPERFAMILY SSF56059 Glutathione synthetase ATP-binding domain-like
197 390 Gene3D G3DSA:3.30.470.20 -
123 294 Pfam PF02222 ATP-grasp domain
123 294 InterPro IPR003135 ATP-grasp fold, ATP-dependent carboxylate-amine ligase-type
2 122 Gene3D G3DSA:3.40.50.20 -
1 391 PANTHER PTHR43055 FORMATE-DEPENDENT PHOSPHORIBOSYLGLYCINAMIDE FORMYLTRANSFERASE

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_A0A0H3GQ50
AlphaFold — — full sequence — Viewing
ColabFold KP13_01608
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 0.36

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 24.83 0.901
2 9.22 0.494

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.

58 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
A12
4MAM
Q5NGE8 425.2 Da LogP -1.64 TPSA 223.4 2 viol. ✓ Clean c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)…
ACP
1KJI
P33221 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)…
AGS
1KJJ
P33221 523.2 Da LogP -1.51 TPSA 262.1 3 viol. ✓ Clean c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)…
AIR
3K5I
A1CII2 295.2 Da LogP -1.81 TPSA 160.3 ✓ Ro5 ✓ Clean c1c(n(cn1)[C@H]2[C@@H]([C@@H]([C@H](O2)COP(=O)(…
ANP
1EYZ
P33221 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)…
GAR
1EZ1
P33221 284.2 Da LogP -4.65 TPSA 177.2 ✓ Ro5 ✓ Clean C([C@@H]1[C@H]([C@H]([C@@H](O1)NC(=O)CN)O)O)OP(…
NHE
3K5I
A1CII2 207.3 Da LogP 0.80 TPSA 66.4 ✓ Ro5 ✓ Clean C1CCC(CC1)NCCS(=O)(=O)O
POP
3ORQ
A0A0H3KFM7 176.0 Da LogP -2.08 TPSA 129.9 ✓ Ro5 ✓ Clean O[P@@](=O)([O-])O[P@@](=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.