Protein profile

PA5163

glucose-1-phosphate thymidylyltransferase

Genome: NC_002516.2

Gene: PA5163 rmlA Structure source: Experimental + AlphaFold UniProt Q9HU22
Amino acids 293
Annotations 10
Features 18
PDB binders 29
Druggability 0.422

Overview

Basic information about this protein and its source genome.

Accession
PA5163
Gene
PA5163 rmlA
Status
annotated
Amino acids
293
Structure source
Experimental + AlphaFold

Target profile

Computed evidence for target prioritization.

Human off-target
hit
Human identity (%)
39.286
Human E-value
9.03e-08
Gut microbiome off-target
hit
Essential (DEG)
Y
Localization
Cytoplasmic

Selected Druggability evidence

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 0.422
Structure
Pocket

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:0005829 The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
  • GO:0008879 Catalysis of the reaction: alpha-D-glucose 1-phosphate + dTTP = diphosphate + dTDP-glucose.
  • GO:0046872 Binding to a metal ion.
  • GO:0000166 Binding to a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
  • GO:0019305 The chemical reactions and pathways resulting in the formation of dTDP-rhamnose, a substance composed of rhamnose in glycosidic linkage with deoxyribosylthymine diphosphate.
  • GO:0009244 The chemical reactions and pathways resulting in the formation of the core region of bacterial lipopolysaccharides, which contains ten saccharide residues.
  • GO:0000271 The chemical reactions and pathways resulting in the formation of a polysaccharide, a polymer of many (typically more than 10) monosaccharide residues linked glycosidically.
  • 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:0045226 OBSOLETE. The chemical reactions and pathways resulting in the formation of polysaccharides used in extracellular structures.

Sequence Features

Domain/signature hits from InterPro and related databases.

18 records
Show feature table
Start End DB Term Name
1 293 Gene3D G3DSA:3.90.550.10 Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A
1 293 InterPro IPR029044 Nucleotide-diphospho-sugar transferases
17 24 Phobius SIGNAL_PEPTIDE_C_REGION C-terminal region of a signal peptide.
1 288 SUPERFAMILY SSF53448 Nucleotide-diphospho-sugar transferases
1 288 InterPro IPR029044 Nucleotide-diphospho-sugar transferases
3 242 CDD cd02538 G1P_TT_short
3 242 InterPro IPR005907 Glucose-1-phosphate thymidylyltransferase, short form
25 293 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
5 16 Phobius SIGNAL_PEPTIDE_H_REGION Hydrophobic region of a signal peptide.
1 4 Phobius SIGNAL_PEPTIDE_N_REGION N-terminal region of a signal peptide.
4 240 Pfam PF00483 Nucleotidyl transferase
4 240 InterPro IPR005835 Nucleotidyl transferase domain
1 24 Phobius SIGNAL_PEPTIDE Signal peptide region
4 290 PANTHER PTHR43532 GLUCOSE-1-PHOSPHATE THYMIDYLYLTRANSFERASE
4 290 InterPro IPR005907 Glucose-1-phosphate thymidylyltransferase, short form
1 293 FunFam G3DSA:3.90.550.10:FF:000023 Glucose-1-phosphate thymidylyltransferase
4 288 NCBIfam TIGR01207 glucose-1-phosphate thymidylyltransferase RfbA
4 288 InterPro IPR005907 Glucose-1-phosphate thymidylyltransferase, short form

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

29 + 1

Experimental PDB entries and predicted models. Click Switch to display a different structure in the viewer.

Entry Method Resolution Chain Coverage Links Status
PDB 5FUH
X-ray 1.60 Å A,B,C,D
100.0% 1-293
Viewing
PDB 1FXO
X-ray 1.66 Å A,B,C,D,E,F,G,H
100.0% 1-293
Loaded
PDB 4B2X
X-ray 1.70 Å A,B,C,D
100.0% 1-293
Loaded
PDB 1G1L
X-ray 1.77 Å A,B,C,D,E,F,G,H
100.0% 1-293
Loaded
PDB 4B3U
X-ray 1.80 Å A,B,C,D
100.0% 1-293
Loaded
PDB 1G0R
X-ray 1.87 Å A,B,C,D,E,F,G,H
100.0% 1-293
Loaded
PDB 1FZW
X-ray 1.90 Å A,B,C,D,E,F,G,H
100.0% 1-293
Loaded
PDB 5FU0
X-ray 1.90 Å A,B,C,D
100.0% 1-293
Loaded
PDB 3ZLK
X-ray 1.95 Å A,B,C,D
100.0% 1-293
Loaded
PDB 3ZLL
X-ray 2.00 Å A,B,C,D
100.0% 1-293
Loaded
PDB 4B5B
X-ray 2.06 Å A,B,C,D
100.0% 1-293
Loaded
PDB 6T37
X-ray 2.08 Å A,B,C,D
100.0% 1-293
Loaded
PDB 4B4B
X-ray 2.10 Å A,B,C,D
100.0% 1-293
Loaded
PDB 6T38
X-ray 2.15 Å A,B,C,D
100.0% 1-293
Loaded
PDB 4ARW
X-ray 2.20 Å A,B,C,D
100.0% 1-293
Loaded
PDB 5FTS
X-ray 2.20 Å A,B,C,D
100.0% 1-293
Loaded
PDB 5FU8
X-ray 2.20 Å A,B,C,D
100.0% 1-293
Loaded
PDB 5FTV
X-ray 2.21 Å A,B,C,D
100.0% 1-293
Loaded
PDB 4ASJ
X-ray 2.25 Å A,B,C,D
100.0% 1-293
Loaded
PDB 4ASY
X-ray 2.30 Å A,B,C,D
100.0% 1-293
Loaded
PDB 4B4M
X-ray 2.35 Å A,B,C,D
100.0% 1-293
Loaded
PDB 4B2W
X-ray 2.36 Å A,B,C,D
100.0% 1-293
Loaded
PDB 5FYE
X-ray 2.40 Å A,B,C,D
100.0% 1-293
Loaded
PDB 6TQG
X-ray 2.45 Å A,B,C,D
100.0% 1-293
Loaded
PDB 4B42
X-ray 2.50 Å A,B,C,D
100.0% 1-293
Loaded
PDB 4B4G
X-ray 2.50 Å A,B,C,D
100.0% 1-293
Loaded
PDB 1G2V
X-ray 2.60 Å A,B,C,D,E,F,G,H
100.0% 1-293
Loaded
PDB 1G3L
X-ray 2.70 Å A,B,C,D
100.0% 1-293
Loaded
PDB 1G23
X-ray 2.80 Å A,B,C,D,E,F,G,H
100.0% 1-293
Loaded
AlphaFold PA5163
AlphaFold 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
5 0.422
10 0.267

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 19.06 0.834
2 8.8 0.471
3 2.08 0.047
4 1.72 0.03

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.

79 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.

Show only:
Ligand Source crystal MW · LogP · TPSA Lipinski PAINS SMILES
4WF 233.2 Da LogP -0.13 TPSA 101.1 ✓ Ro5 ✓ Clean c1ccc(cc1)CN2C(=C(C(=O)NC2=O)N)O
942 316.4 Da LogP 1.20 TPSA 101.2 ✓ Ro5 ✓ Clean CCCCN1C(=C(C(=O)NC1=O)N(C)C(=O)c2ccccc2)N
BBE 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 336.4 Da LogP 1.42 TPSA 110.0 ✓ Ro5 ✓ Clean c1ccc(cc1)CN2C(=C(C(=O)NC2=O)NC(=O)c3ccccc3)N
DAU 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@]…
DH5 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…
FKH 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…
GJB 232.2 Da LogP 0.70 TPSA 66.5 ✓ Ro5 ✓ Clean c1ccc(cc1)CCN2C(=O)CC(=O)NC2=O
HKX 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 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 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 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 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 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 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 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 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 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 266.3 Da LogP 1.27 TPSA 92.9 ✓ Ro5 ✓ Clean CCCCN1C(=C(C(=O)NC1=O)NC2CCCC2)N
NVQ 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 260.3 Da LogP 0.60 TPSA 92.9 ✓ Ro5 ✓ Clean CCNC1=C(N(C(=O)NC1=O)Cc2ccccc2)N
P3I 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…
TRH 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 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@]…
Y46 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.