KpKP13 Protein target profile

Orotate phosphoribosyltransferase

Accession: KP13_31497

Gene: pyrE AHE42096.1 3D evidence: AlphaFold DB model + ColabFold model UniProt A0A0H3GXD7
Length 213
Pocket druggability (P2Rank · AlphaFold DB model) 0.075
Direct ligand evidence 0 74 total records
Functional annotation 1 EC 7 GO
Target summary

Target candidate with partial support; inspect missing evidence before prioritizing.

Automated synthesis of the evidence currently loaded. Review the underlying records before prioritizing this protein.

Terms and data sources used on this page

PDB: experimentally determined structures from the Protein Data Bank. These are the strongest structural evidence, but may cover only part of the protein.

AlphaFold DB model: a precomputed predicted structure downloaded from AlphaFold Database/UniProt, not an experiment performed here.

ColabFold model: a predicted structure generated for this workspace; interpret it with coverage and confidence.

pLDDT: confidence score for predicted structures. High values support local geometry; low values mean the region should not drive pocket interpretation.

FPocket / P2Rank: software tools that predict possible ligand-binding pockets on a 3D structure. They are useful screening signals, not experimental validation.

Druggability: a pocket-based estimate of whether a small molecule could bind productively. It does not mean a drug already exists.

PDB ligand: a compound observed in an experimental structure. Direct same-protein records are stronger than homolog-transferred records.

ChEMBL: a public database of measured compound bioactivity. Direct entries are stronger than entries transferred from similar proteins.

ZINC: a purchasable-compound database. Here it marks proposed candidates from chemical similarity, not measured binders.

LigQ / LigQ_2: an internal Target pipeline step that gathers PDB, ChEMBL, and ZINC ligand evidence for each protein.

Off-target: sequence similarity to proteins we prefer not to hit, such as human proteins or beneficial gut microbiome proteins.

DEG: Database of Essential Genes. A match suggests the protein resembles genes known to be essential in other organisms.

Roary / CoreCruncher: pan-genome tools used to decide whether a gene is core across analyzed strains or accessory/strain-specific.

EC / GO: functional annotations: EC describes enzyme reactions; GO describes biological process, molecular function, or cellular component.

KEGG pathway: a curated metabolic route label used here to group reactions imported from the metabolic model.

Chokepoint: a metabolic reaction that is the only producer or consumer of a metabolite in the imported model.

Prioritization evidence

Selectivity, essentiality, structural confidence, conservation, and predicted binding-site evidence.

Off-target risk

Human off-target
Hit
Human identity (%)
31.183 Lower values reduce human off-target concern.
Human E-value
3.16e-08
Gut microbiome similarity
6.5% of screened genomes Lower prevalence suggests narrower overlap with the screened gut microbiome.

Essentiality

Essential (DEG)
Y
DEG identity (%)
70.423 Higher values support similarity to known essential genes.
DEG E-value
4.0700000000000003e-107 Smaller values mean stronger essential-gene similarity.

Structure confidence

ColabFold pLDDT
95.77 0-100 confidence; >70 supports local structural interpretation.

Binding-site evidence

AlphaFold DB / UniProt model

P2Rank's binding-site probability is the primary druggability signal shown across the app; FPocket's druggability score is shown alongside it for comparison. Both estimate small-molecule pocket quality after applying the curated structure priority — neither is experimental binding evidence. The 3D viewer may show a different loaded structure, so visible pockets can differ.

Druggability (P2Rank) 0.075
Structure A0A0H3GXD7
Pocket Pocket 1
Druggability (FPocket) 0.116
Structure A0A0H3GXD7
Pocket Pocket 11
ColabFold model
P2Rank 0.069 · Pocket 1
FPocket 0.034 · Pocket 7
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 306 / 4744 genomes with a hit
Prevalence 6.5%

Sequence

Primary amino-acid sequence viewer.

MKPYQRQFIEFALSKQVLKFGEFTLKSGRKSPYFFNAGLFNTGRDLALLGRFYAEALVDSGIEFDLLFGPAYKGIPIATTTAVALAEHHDRDLPYCFNRKEAKTHGEGGNLVGSPLQGRVMLVDDVITAGTAIRESMEIIQAQGAQLAGVLISLDRQERGRGEISAIQEVERDYGCQVISIITLKELITYLEEKPEMAEHLASVRAYREAYGV

Functional annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 7 GO

Subcellular localization

Localization
Cytoplasmic

Enzyme Commission (EC)

1

Gene Ontology (GO)

7
  • GO:0004588 Catalysis of the reaction: orotidine 5'-phosphate + diphosphate = orotate + 5-phospho-alpha-D-ribose 1-diphosphate.
  • GO:0006221 The chemical reactions and pathways resulting in the formation of a pyrimidine nucleotide, a compound consisting of nucleoside (a pyrimidine 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:0005737 The contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
  • GO:0000287 Binding to a magnesium (Mg) ion.
  • GO:0006207 The chemical reactions and pathways resulting in the formation of pyrimidine nucleobases, 1,3-diazine, organic nitrogenous bases, beginning with the synthesis of a pyrimidine ring from simpler precursors.
  • GO:0044205 The chemical reactions and pathways resulting in the formation of UMP, uridine monophosphate, starting with the synthesis of (S)-dihydroorotate from bicarbonate; UMP biosynthesis may either occur via reduction by quinone, NAD+ or oxygen.
  • GO:0046132 The chemical reactions and pathways resulting in the formation of any ribonucleoside, a nucleoside in which a pyrimidine base is linked to a ribose (beta-D-ribofuranose) molecule.

Sequence domains and features

Domain and signature matches imported from InterPro and related databases.

14 records
Show feature table
Start End DB Term Name
10 187 NCBIfam TIGR00336 orotate phosphoribosyltransferase
10 187 InterPro IPR004467 Orotate phosphoribosyl transferase domain
1 213 PANTHER PTHR46683 OROTATE PHOSPHORIBOSYLTRANSFERASE 1-RELATED
2 211 SUPERFAMILY SSF53271 PRTase-like
2 211 InterPro IPR029057 Phosphoribosyltransferase-like
1 213 Gene3D G3DSA:3.40.50.2020 -
1 213 InterPro IPR029057 Phosphoribosyltransferase-like
50 159 Pfam PF00156 Phosphoribosyl transferase domain
50 159 InterPro IPR000836 Phosphoribosyltransferase domain
1 213 Hamap MF_01208 Orotate phosphoribosyltransferase [pyrE].
1 213 InterPro IPR023031 Orotate phosphoribosyltransferase
1 213 FunFam G3DSA:3.40.50.2020:FF:000008 Orotate phosphoribosyltransferase
49 174 CDD cd06223 PRTases_typeI
49 174 InterPro IPR000836 Phosphoribosyltransferase domain

3D structure

Selected loaded structure. Experimental PDB entries may cover only a portion of the sequence; AlphaFold DB and ColabFold models typically cover the full protein but remain computational predictions.

Download VMD script Full viewer

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Pocket score High Medium Low
How colors and pocket overlays are used
Uniform protein color marks the displayed model as a single molecular object.
Experimental PDB structures may be colored by chain to distinguish subunits or copies present in the file.
Pocket colors and alpha spheres are evidence overlays for predicted binding cavities; they are not alternative protein chains.
'Alpha spheres' is FPocket's own cavity-shape geometry, imported when available and aligned with the loaded structure.
'Pocket atoms'/'Predicted site atoms' show the pocket's residue atoms instead: P2Rank reports residues rather than alpha spheres, and FPocket falls back to this when alpha-sphere geometry is unavailable or doesn't align.
'No pocket geometry' means neither alpha spheres nor residue-position data could be found for that pocket; the layer just highlights the same residues as 'Nearby residues'.
Pocket details Inspect a specific pocket, or open the full viewer

Binding pockets · P2Rank

Druggability (P2Rank): high ≥ 0.5 · medium 0.2–0.49 · low < 0.2

Pocket 1 P2Rank #1
0.075
Show in viewer
Surrounding area
Pocket 2 P2Rank #2
0.038
Show in viewer
Surrounding area
Pocket 3 P2Rank #3
0.018
Show in viewer
Surrounding area
Residue sets
UniProt: Binding site:100-100 in other chain
UniProt: Binding site:103-103
UniProt: Binding site:105-105
UniProt: Binding site:124-132 in other chain
UniProt: Binding site:128-128
UniProt: Binding site:156-156
UniProt: Binding site:26-26 in other chain
UniProt: Binding site:34-35
UniProt: Binding site:72-73 in other chain
UniProt: Binding site:99-99
All structural evidence 0 experimental · 2 predicted

Structural evidence

0 + 2

Experimental PDB entries plus predicted AlphaFold DB or ColabFold models. Click Switch to display a different loaded structure in the viewer.

Entry Method Resolution Chain Coverage Links Status
AlphaFold DB AF_A0A0H3GXD7
AlphaFold DB full sequence Viewing
ColabFold KP13_31497
ColabFold full sequence Loaded

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.

74 records
Chemistry signal

Structural and bioactivity evidence are both available for this target.

Direct evidence 0 same-protein records
Transferred evidence 24 records from similar proteins
Structural ligands 20 0 loaded crystals
Measured bioactivity 4 direct and transferred ChEMBL records
Proposed compounds 50 similarity-based ZINC candidates
Best available ligand signal
5BU PDB via homolog 403.1 Da · LogP -1.97 · TPSA 171.3 Open detail RCSB PDB
5FU PDB via homolog Detail RCSB PDB
5IU PDB via homolog Detail RCSB PDB
6AU PDB via homolog Detail RCSB PDB
6CN PDB via homolog Detail RCSB PDB

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
5BU RCSB PDB P11172 403.1 Da LogP -1.97 TPSA 171.3 ✓ Ro5 ✓ Clean C1=C(C(=O)NC(=O)N1[C@H]2[C@@H]([C@@H]([C@H](O2)…
5FU RCSB PDB P11172 342.2 Da LogP -2.60 TPSA 171.3 ✓ Ro5 ✓ Clean C1=C(C(=O)NC(=O)N1[C@H]2[C@@H]([C@@H]([C@H](O2)…
5IU RCSB PDB P11172 434.1 Da LogP -1.10 TPSA 151.1 ✓ Ro5 ✓ Clean C1[C@@H]([C@H](O[C@H]1N2C=C(C(=O)NC2=O)I)COP(=O…
6AU RCSB PDB P11172 366.2 Da LogP -2.53 TPSA 188.4 ✓ Ro5 ✓ Clean CC(=O)C1=CC(=O)NC(=O)N1[C@H]2[C@@H]([C@@H]([C@H…
6CN RCSB PDB P11172 349.2 Da LogP -2.86 TPSA 195.1 ✓ Ro5 ✓ Clean C1=C(N(C(=O)NC1=O)C2C(C(C(O2)COP(=O)(O)O)O)O)C#N
6ZJ RCSB PDB P9WHK9 434.0 Da LogP -2.96 TPSA 198.3 1 viol. ✓ Clean C1C(=O)O[Fe]234(OC(=O)CC1(C(=O)O2)O)OC(=O)CC(CC…
BMP RCSB PDB P11172 340.2 Da LogP -3.03 TPSA 191.5 1 viol. ✓ Clean C1=C(N(C(=O)NC1=O)[C@H]2[C@@H]([C@@H]([C@H](O2)…
CNU RCSB PDB P11172 349.2 Da LogP -2.86 TPSA 195.1 ✓ Ro5 ✓ Clean C1=C(C(=O)NC(=O)N1C2C(C(C(O2)COP(=O)(O)O)O)O)C#N
JW5 RCSB PDB P11172 354.2 Da LogP -3.24 TPSA 191.5 1 viol. ✓ Clean C1=C(N(C(=O)NC1=O)[C@H]2[C@@H]([C@@H]([C@H](O2)…
NUP RCSB PDB P11172 339.2 Da LogP -3.15 TPSA 197.3 1 viol. ✓ Clean C1=C(N(C(=O)NC1=O)[C@H]2[C@@H]([C@@H]([C@H](O2)…
OMP RCSB PDB P08870 368.2 Da LogP -3.04 TPSA 208.6 1 viol. ✓ Clean C1=C(N(C(=O)NC1=O)[C@H]2[C@@H]([C@@H]([C@H](O2)…
PFU RCSB PDB P11172 339.2 Da LogP -2.51 TPSA 208.4 1 viol. ✓ Clean C([C@@H]1[C@H]([C@H]([C@@H](O1)c2c(c([nH]n2)C(=…
QRT RCSB PDB P11172 367.2 Da LogP -3.64 TPSA 214.4 1 viol. ✓ Clean C1=C(N(C(=O)NC1=O)[C@H]2[C@@H]([C@@H]([C@H](O2)…
QRZ RCSB PDB P11172 383.3 Da LogP -3.10 TPSA 197.3 1 viol. ✓ Clean C1=C(N(C(=O)NC1=O)[C@H]2[C@@H]([C@@H]([C@H](O2)…
S5P RCSB PDB P11172 356.2 Da LogP -2.45 TPSA 171.3 1 viol. ✓ Clean C1=C(N(C(=O)NC1=O)[C@H]2[C@@H]([C@@H]([C@H](O2)…
U RCSB PDB P11172 324.2 Da LogP -2.73 TPSA 171.3 ✓ Ro5 ✓ Clean C1=CN(C(=O)NC1=O)[C@H]2[C@@H]([C@@H]([C@H](O2)C…
U1P RCSB PDB P11172 351.2 Da LogP -2.74 TPSA 195.2 1 viol. ✓ Clean [H]/N=C/C1=CC(=O)NC(=O)N1[C@H]2[C@@H]([C@@H]([C…
UEP RCSB PDB P11172 352.2 Da LogP -2.17 TPSA 171.3 ✓ Ro5 ✓ Clean CCC1=CC(=O)NC(=O)N1[C@H]2[C@@H]([C@@H]([C@H](O2…
UFT RCSB PDB P11172 326.2 Da LogP -1.76 TPSA 151.1 ✓ Ro5 ✓ Clean C1=CN(C(=O)NC1=O)[C@H]2[C@@H]([C@@H]([C@H](O2)C…
XMP RCSB PDB P11172 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(=…

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.

Cross-references

External database identifiers for this protein, its structures, ligands, and metabolic reactions.