KpKP13 Protein target profile

Glucose-1-phosphate thymidylyltransferase in cps region

Accession: KP13_03797

Gene: AHE43665.1 rmlA 3D evidence: AlphaFold DB model + ColabFold model UniProt A0A0H3GQN6
Length 289
Pocket druggability (P2Rank · AlphaFold DB model) 0.908
Direct ligand evidence 0 81 total records
Functional annotation 1 EC 4 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 (%)
34.545 Lower values reduce human off-target concern.
Human E-value
3.05e-07
Gut microbiome similarity
49.9% of screened genomes Lower prevalence suggests narrower overlap with the screened gut microbiome.

Essentiality

Essential (DEG)
Y
DEG identity (%)
75.433 Higher values support similarity to known essential genes.
DEG E-value
9.160000000000001e-167 Smaller values mean stronger essential-gene similarity.

Structure confidence

ColabFold pLDDT
96.72 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) 0.908
Structure A0A0H3GQN6
Pocket Pocket 1
Druggability (FPocket) 0.309
Structure A0A0H3GQN6
Pocket Pocket 17
ColabFold model
P2Rank 0.902 · Pocket 1
FPocket 0.626 · Pocket 2
Core conservation Accessory gene
Roary accessory
CoreCruncher accessory
Gut microbiome 2366 / 4744 genomes with a hit
Prevalence 49.9%

Sequence

Primary amino-acid sequence viewer.

MKGIVLAGGSGTRLYPITQGVSKQLLPIYDKPMIFYPVSVLMLAGIRDILIISTPDDMPSFQRLLGDGSQFGVNFSYAIQPSPDGLAQAFIIGEKFIGNDACALVLGDNIYFGQSFGKKLEAAAAKTSGATVFGYQVLDPERFGVVEFDENYKALSIEEKPLKPKSDWAVTGLYFYDNNVVEMAKDVKPSERGELEITTLNQMYLERGDLQVELLGRGFAWLDTGTHDSLMDASQFIHTIEKRQGMKVACLEEIAYRNQWLSAEGVAVQAERLKKTEYGAYLKRLLNER

Functional annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 4 GO

Subcellular localization

Localization
Cytoplasmic

Enzyme Commission (EC)

1

Gene Ontology (GO)

4
  • GO:0045226 OBSOLETE. The chemical reactions and pathways resulting in the formation of polysaccharides used in extracellular structures.
  • GO:0009058 A cellular process consisting of the biochemical pathways by which a living organism synthesizes chemical substances. This typically represents the energy-requiring part of metabolism in which simpler substances are transformed into more complex ones.
  • GO:0008879 Catalysis of the reaction: alpha-D-glucose 1-phosphate + dTTP = diphosphate + dTDP-glucose.
  • GO:0046872 Binding to a metal ion.

Sequence domains and features

Domain and signature matches imported from InterPro and related databases.

16 records
Show feature table
Start End DB Term Name
54 289 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm.
1 289 Gene3D G3DSA:3.90.550.10 Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A
1 289 InterPro IPR029044 Nucleotide-diphospho-sugar transferases
2 238 Pfam PF00483 Nucleotidyl transferase
2 238 InterPro IPR005835 Nucleotidyl transferase domain
34 53 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
1 289 FunFam G3DSA:3.90.550.10:FF:000023 Glucose-1-phosphate thymidylyltransferase
2 286 NCBIfam TIGR01207 glucose-1-phosphate thymidylyltransferase RfbA
2 286 InterPro IPR005907 Glucose-1-phosphate thymidylyltransferase, short form
1 240 CDD cd02538 G1P_TT_short
1 240 InterPro IPR005907 Glucose-1-phosphate thymidylyltransferase, short form
1 288 PANTHER PTHR43532 GLUCOSE-1-PHOSPHATE THYMIDYLYLTRANSFERASE
1 288 InterPro IPR005907 Glucose-1-phosphate thymidylyltransferase, short form
1 287 SUPERFAMILY SSF53448 Nucleotide-diphospho-sugar transferases
1 287 InterPro IPR029044 Nucleotide-diphospho-sugar transferases
1 33 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.

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.

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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
0.908
Show in viewer
Surrounding area
Pocket 2 P2Rank #2
0.277
Show in viewer
Surrounding area
Pocket 3 P2Rank #3
0.064
Likely same site as FPocket 17 2.1 Å 11 shared residues 100% of smaller site
Show in viewer
Surrounding area

Binding pockets · FPocket

Druggability (FPocket): high ≥ 0.7 · medium 0.4–0.69 · low < 0.4

Pocket 1 FPocket #17
0.309
Likely same site as P2Rank 3 2.1 Å 11 shared residues 100% of smaller site
Show in viewer
Surrounding area
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_A0A0H3GQN6
AlphaFold DB full sequence Viewing
ColabFold KP13_03797
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.

81 records
Chemistry signal

Structural ligand evidence is available for this target.

Direct evidence 0 same-protein records
Transferred evidence 31 records from similar proteins
Structural ligands 31 0 loaded crystals
Measured bioactivity 0 direct and transferred ChEMBL records
Proposed compounds 50 similarity-based ZINC candidates
Best available ligand signal
4WF PDB via homolog 233.2 Da · LogP -0.13 · TPSA 101.1 Open detail RCSB PDB
942 PDB via homolog Detail RCSB PDB
BBE PDB via homolog Detail RCSB PDB
BZ0 PDB via homolog Detail RCSB PDB
DAU 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
4WF RCSB PDB Q9HU22 233.2 Da LogP -0.13 TPSA 101.1 ✓ Ro5 ✓ Clean c1ccc(cc1)CN2C(=C(C(=O)NC2=O)N)O
942 RCSB PDB Q9HU22 316.4 Da LogP 1.20 TPSA 101.2 ✓ Ro5 ✓ Clean CCCCN1C(=C(C(=O)NC1=O)N(C)C(=O)c2ccccc2)N
BBE RCSB PDB Q9HU22 400.5 Da LogP 1.30 TPSA 118.3 ✓ Ro5 ✓ Clean Cc1cccc(c1)S(=O)(=O)N(C)C2=C(N(C(=O)NC2=O)Cc3cc…
BZ0 RCSB PDB Q9HU22 336.4 Da LogP 1.42 TPSA 110.0 ✓ Ro5 ✓ Clean c1ccc(cc1)CN2C(=C(C(=O)NC2=O)NC(=O)c3ccccc3)N
DAU RCSB PDB Q9AGY4 564.3 Da LogP -3.46 TPSA 276.8 3 viol. ✓ Clean CC1=CN(C(=O)NC1=O)[C@H]2C[C@@H]([C@H](O2)CO[P@]…
DGT RCSB PDB P26393 507.2 Da LogP -1.31 TPSA 278.9 3 viol. ✓ Clean c1nc2c(n1[C@H]3C[C@@H]([C@H](O3)CO[P@@](=O)(O)O…
DH5 RCSB PDB Q9HU22 479.4 Da LogP 2.06 TPSA 118.3 ✓ Ro5 ✓ Clean Cc1cc(ccc1Br)CN2C(=C(C(=O)NC2=O)N(C)S(=O)(=O)c3…
DTP RCSB PDB P26393 491.2 Da LogP -0.60 TPSA 258.9 2 viol. ✓ Clean c1nc(c2c(n1)n(cn2)[C@H]3C[C@@H]([C@H](O3)CO[P@]…
FKH RCSB PDB Q9HU22 400.5 Da LogP 1.30 TPSA 118.3 ✓ Ro5 ✓ Clean Cc1cccc(c1)CN2C(=C(C(=O)NC2=O)N(C)S(=O)(=O)c3cc…
GDU RCSB PDB Q9AGY4 566.3 Da LogP -4.79 TPSA 297.0 3 viol. ✓ Clean C1=CN(C(=O)NC1=O)[C@H]2[C@@H]([C@@H]([C@H](O2)C…
GJB RCSB PDB Q9HU22 232.2 Da LogP 0.70 TPSA 66.5 ✓ Ro5 ✓ Clean c1ccc(cc1)CCN2C(=O)CC(=O)NC2=O
HKX RCSB PDB Q9HU22 465.3 Da LogP 1.75 TPSA 118.3 ✓ Ro5 ✓ Clean CN(C1=C(N(C(=O)NC1=O)Cc2cccc(c2)Br)N)S(=O)(=O)c…
HNR RCSB PDB Q9HU22 352.4 Da LogP 0.74 TPSA 118.3 ✓ Ro5 ✓ Clean CCCCN1C(=C(C(=O)NC1=O)N(C)S(=O)(=O)c2ccccc2)N
JWT RCSB PDB Q9HU22 404.4 Da LogP 1.13 TPSA 118.3 ✓ Ro5 ✓ Clean CN(C1=C(N(C(=O)NC1=O)Cc2ccccc2)N)S(=O)(=O)c3ccc…
KDT RCSB PDB Q9HU22 465.3 Da LogP 1.75 TPSA 118.3 ✓ Ro5 ✓ Clean CN(C1=C(N(C(=O)NC1=O)Cc2ccc(cc2)Br)N)S(=O)(=O)c…
KKT RCSB PDB Q9HU22 366.4 Da LogP 0.73 TPSA 118.3 ✓ Ro5 ✓ Clean CCCCS(=O)(=O)N(C)C1=C(N(C(=O)NC1=O)Cc2ccccc2)N
LD6 RCSB PDB Q9HU22 404.4 Da LogP 1.13 TPSA 118.3 ✓ Ro5 ✓ Clean CN(C1=C(N(C(=O)NC1=O)Cc2cccc(c2)F)N)S(=O)(=O)c3…
M9Z RCSB PDB Q9HU22 524.6 Da LogP 0.96 TPSA 161.0 1 viol. ✓ Clean CN(C1=C(N(C(=O)NC1=O)Cc2ccccc2)NCCCn3cc(nn3)CN)…
MBK RCSB PDB Q9HU22 536.5 Da LogP 2.32 TPSA 130.3 1 viol. ✓ Clean CN(C1=C(N(C(=O)NC1=O)Cc2ccc(cc2)Br)NCCCCN)S(=O)…
N5Y RCSB PDB Q9HU22 350.4 Da LogP 1.44 TPSA 101.2 ✓ Ro5 ✓ Clean CN(C1=C(N(C(=O)NC1=O)Cc2ccccc2)N)C(=O)c3ccccc3
N6A RCSB PDB Q9HU22 386.4 Da LogP 0.99 TPSA 118.3 ✓ Ro5 ✓ Clean CN(C1=C(N(C(=O)NC1=O)Cc2ccccc2)N)S(=O)(=O)c3ccc…
NIQ RCSB PDB Q9HU22 266.3 Da LogP 1.27 TPSA 92.9 ✓ Ro5 ✓ Clean CCCCN1C(=C(C(=O)NC1=O)NC2CCCC2)N
NVQ RCSB PDB Q9HU22 536.5 Da LogP 2.19 TPSA 116.3 1 viol. ✓ Clean CNCCCNC1=C(C(=O)NC(=O)N1Cc2ccc(cc2)Br)N(C)S(=O)…
NWL RCSB PDB Q9HU22 260.3 Da LogP 0.60 TPSA 92.9 ✓ Ro5 ✓ Clean CCNC1=C(N(C(=O)NC1=O)Cc2ccccc2)N
P3I RCSB PDB Q9HU22 465.3 Da LogP 1.75 TPSA 118.3 ✓ Ro5 ✓ Clean CN(C1=C(N(C(=O)NC1=O)Cc2ccccc2Br)N)S(=O)(=O)c3c…
THM RCSB PDB Q9AGY4 242.2 Da LogP -1.51 TPSA 104.6 ✓ Ro5 ✓ Clean CC1=CN(C(=O)NC1=O)[C@H]2C[C@@H]([C@H](O2)CO)O
TRH RCSB PDB Q9HU22 548.3 Da LogP -2.43 TPSA 256.5 3 viol. ✓ Clean C[C@H]1[C@@H]([C@H]([C@H]([C@H](O1)O[P@](=O)(O)…
TTP RCSB PDB Q9HU22 482.2 Da LogP -1.16 TPSA 244.1 2 viol. ✓ Clean CC1=CN(C(=O)NC1=O)[C@H]2C[C@@H]([C@H](O2)CO[P@]…
UD1 RCSB PDB Q9AGY4 607.4 Da LogP -4.65 TPSA 305.9 3 viol. ✓ Clean CC(=O)N[C@@H]1[C@H]([C@@H]([C@H](O[C@@H]1O[P@@]…
UPG RCSB PDB P26393 566.3 Da LogP -4.79 TPSA 297.0 3 viol. ✓ Clean C1=CN(C(=O)NC1=O)[C@H]2[C@@H]([C@@H]([C@H](O2)C…
Y46 RCSB PDB Q9HU22 372.4 Da LogP 0.97 TPSA 127.0 ✓ Ro5 ✓ Clean c1ccc(cc1)CN2C(=C(C(=O)NC2=O)NS(=O)(=O)c3ccccc3…

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.