Protein profile

KP13_05358

Tryptophan synthase beta chain

Genome: KpKP13

Gene: trpB AHE45005.1 Structure source: AlphaFold + ColabFold UniProt A0A0H3GNB7
Amino acids 397
Annotations 5
Features 22
PDB binders 41
Druggability 0.945

Overview

Basic information about this protein and its source genome.

Accession
KP13_05358
Gene
trpB AHE45005.1
Status
annotated
Amino acids
397
Structure source
AlphaFold + ColabFold

Target profile

Computed evidence for target prioritization.

Human off-target
No hit
Human identity (%)
0.0
Gut microbiome off-target
hit
Essential (DEG)
Y
DEG identity (%)
83.077
DEG E-value
0.0
Localization
Cytoplasmic
ColabFold pLDDT
97.56

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 0.945
Structure A0A0H3GNB7
Pocket Pocket 1
P2Rank 0.931
Structure A0A0H3GNB7
Pocket Pocket 1
ColabFold model
FPocket 0.934 · Pocket 1
P2Rank 0.89 · Pocket 1
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 1748 / 4744 genomes with a hit
Normalized 0.368

Sequence

Primary amino-acid sequence viewer.

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 4 GO

Enzyme Commission (EC)

1

Gene Ontology (GO)

4
  • GO:0004834 Catalysis of the reaction: L-serine + (1S,2R)-1-C-(indol-3-yl)glycerol 3-phosphate = L-tryptophan + glyceraldehyde 3-phosphate + H2O.
  • GO:0000162 The chemical reactions and pathways resulting in the formation of L-tryptophan, the chiral amino acid 2-amino-3-(1H-indol-3-yl)propanoic acid; L-tryptophan is synthesized from chorismate via anthranilate.
  • GO:0006568 The chemical reactions and pathways involving tryptophan, the chiral amino acid 2-amino-3-(1H-indol-3-yl)propanoic acid.
  • GO:0005737 The contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

Sequence Features

Domain/signature hits from InterPro and related databases.

22 records
Show feature table
Start End DB Term Name
7 392 PANTHER PTHR48077 TRYPTOPHAN SYNTHASE-RELATED
7 392 InterPro IPR023026 Tryptophan synthase beta chain/beta chain-like
8 389 NCBIfam TIGR00263 tryptophan synthase subunit beta
8 389 InterPro IPR006654 Tryptophan synthase, beta chain
80 94 ProSitePatterns PS00168 Tryptophan synthase beta chain pyridoxal-phosphate attachment site.
80 94 InterPro IPR006653 Tryptophan synthase, beta chain, conserved site
9 205 Gene3D G3DSA:3.40.50.1100 -
9 205 InterPro IPR036052 Tryptophan synthase beta chain-like, PALP domain superfamily
23 387 CDD cd06446 Trp-synth_B
23 387 InterPro IPR006654 Tryptophan synthase, beta chain
1 397 PIRSF PIRSF001413 Trp_syn_beta
1 397 InterPro IPR023026 Tryptophan synthase beta chain/beta chain-like
6 390 SUPERFAMILY SSF53686 Tryptophan synthase beta subunit-like PLP-dependent enzymes
6 390 InterPro IPR036052 Tryptophan synthase beta chain-like, PALP domain superfamily
54 385 Gene3D G3DSA:3.40.50.1100 -
54 385 InterPro IPR036052 Tryptophan synthase beta chain-like, PALP domain superfamily
2 391 Hamap MF_00133 Tryptophan synthase beta chain [trpB].
2 391 InterPro IPR023026 Tryptophan synthase beta chain/beta chain-like
52 375 Pfam PF00291 Pyridoxal-phosphate dependent enzyme
52 375 InterPro IPR001926 Tryptophan synthase beta chain-like, PALP domain
205 384 FunFam G3DSA:3.40.50.1100:FF:000004 Tryptophan synthase beta chain
69 204 FunFam G3DSA:3.40.50.1100:FF:000001 Tryptophan synthase beta chain

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_A0A0H3GNB7
AlphaFold full sequence Viewing
ColabFold KP13_05358
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 0.945
7 0.568

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 24.1 0.895
2 2.22 0.054
3 2.16 0.051
4 1.8 0.034
5 0.88 0.004

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.

91 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
0JO P0A2K1 316.2 Da LogP 0.72 TPSA 149.5 ✓ Ro5 ✓ Clean Cc1c(c(c(cn1)COP(=O)(O)O)/C=N/C(=C)C(=O)O)O
13P P0A2K1 170.1 Da LogP -1.34 TPSA 104.1 ✓ Ro5 ✓ Clean C(C(=O)COP(=O)(O)O)O
1D0 P0A2K1 425.3 Da LogP 1.55 TPSA 181.8 1 viol. ✓ Clean Cc1c(c(c(cn1)COP(=O)(O)O)C/N=C(\CNc2ccccc2O)/C(…
78U Q8U093 218.3 Da LogP 1.68 TPSA 79.1 ✓ Ro5 ✓ Clean C[C@@H](c1c[nH]c2c1cccc2)[C@@H](C(=O)O)N
79V P9WFX9 282.3 Da LogP 2.43 TPSA 56.0 ✓ Ro5 ✓ Clean c1ccc(c(c1)c2ccc(cc2)C3C(NC3C#N)CO)F
7MN P0A2K1 436.4 Da LogP -0.07 TPSA 153.5 1 viol. ✓ Clean CC1=C(/C(=C\[NH+]=C(/C[N@@]2CCc3c2cccc3)\C(=O)O…
AQ3 P0A2K1 427.4 Da LogP 1.07 TPSA 181.5 1 viol. ✓ Clean Cc1c(c(c(cn1)COP(=O)(O)O)CN[C@H](CNc2ccccc2O)C(…
BZI P0A2K1 118.1 Da LogP 1.56 TPSA 28.7 ✓ Ro5 ✓ Clean c1ccc2c(c1)[nH]cn2
F6F P0A2K1 329.2 Da LogP 1.42 TPSA 105.1 ✓ Ro5 ✓ Clean c1cc(ccc1C(=O)NCCOP(=O)(O)O)OC(F)(F)F
F9F P0A2K1 365.2 Da LogP 0.97 TPSA 122.2 ✓ Ro5 ✓ Clean c1cc(ccc1OC(F)(F)F)S(=O)(=O)NCCOP(=O)(O)O
FEJ Q8U093 376.3 Da LogP 0.59 TPSA 169.8 ✓ Ro5 ✓ Clean Cc1c(c(c(cn1)COP(=O)(O)O)/C=N/[C@@H]([C@H](C(C)…
FEV Q8U093 344.3 Da LogP 1.50 TPSA 149.5 ✓ Ro5 ✓ Clean CC/C=C(\C(=O)O)/N=C/c1c(cnc(c1O)C)COP(=O)(O)O
FIP P0A2K1 273.2 Da LogP 2.35 TPSA 82.6 ✓ Ro5 ✓ Clean c1cc2c(cc1F)c(c[nH]2)CCCOP(=O)(O)O
G3P P0A2K1 172.1 Da LogP -1.55 TPSA 107.2 ✓ Ro5 ✓ Clean C([C@H](COP(=O)(O)O)O)O
H9V P9WFX9 336.7 Da LogP 4.20 TPSA 35.8 ✓ Ro5 ✓ Clean c1cc(ccc1c2c(cc(cc2F)Cl)F)C3C(NC3C#N)CF
HDJ P9WFX9 316.3 Da LogP 3.86 TPSA 35.8 ✓ Ro5 ✓ Clean Cc1cc(c(c(c1)F)c2ccc(cc2)C3C(NC3C#N)CF)F
HE1 P0A2K1 260.3 Da LogP 2.57 TPSA 77.8 ✓ Ro5 ✓ Clean c1ccc(c(c1)O)SCC\C=C\P(=O)(O)O
HF1 P0A2K1 278.2 Da LogP 2.70 TPSA 77.8 ✓ Ro5 ✓ Clean c1cc(c(cc1F)SCCC=CP(=O)(O)O)O
HPF P0A2K1 279.2 Da LogP -0.41 TPSA 139.5 1 viol. ✓ Clean c1ccc(c(c1)N[C@@H]([C@@H](COP(=O)(O)O)O)O)O
HSP P0A2K1 278.3 Da LogP 1.46 TPSA 94.8 ✓ Ro5 ✓ Clean c1ccc(c(c1)O)[S@](=O)CCCCP(=O)(O)O
IAD P0A2K1 290.3 Da LogP 0.75 TPSA 119.5 ✓ Ro5 ✓ Clean c1ccc2c(c1)c(c[nH]2)CC(=O)N[C@@H](CC(=O)O)C(=O)O
IAG P0A2K1 232.2 Da LogP 0.91 TPSA 82.2 ✓ Ro5 ✓ Clean c1ccc2c(c1)c(c[nH]2)CC(=O)NCC(=O)O
IDM P0A2K1 119.2 Da LogP 1.65 TPSA 12.0 ✓ Ro5 ✓ Clean c1ccc2c(c1)CCN2
IGP P0A2K1 287.2 Da LogP 0.67 TPSA 123.0 ✓ Ro5 ✓ Clean c1ccc2c(c1)c(c[nH]2)[C@@H]([C@@H](COP(=O)(O)O)O…
IPL P0A2K1 255.2 Da LogP 2.21 TPSA 82.6 ✓ Ro5 ✓ Clean c1ccc2c(c1)c(c[nH]2)CCCOP(=O)(O)O
KOU P0A2K1 334.2 Da LogP -0.43 TPSA 169.8 ✓ Ro5 ✓ Clean Cc1c(c(c(cn1)COP(=O)(O)O)/C=N/C(CO)C(=O)O)O
MH6 P0A2K1 103.1 Da LogP -0.92 TPSA 81.4 ✓ Ro5 ✓ Clean [H]/N=C(\CO)/C(=O)O
MLA P9WFX9 104.1 Da LogP -0.45 TPSA 74.6 ✓ Ro5 ✓ Clean C(C(=O)O)C(=O)O
MLI P9WFX9 102.0 Da LogP -3.12 TPSA 80.3 ✓ Ro5 ✓ Clean C(C(=O)[O-])C(=O)[O-]
MLT P9WFX9 134.1 Da LogP -1.09 TPSA 94.8 ✓ Ro5 ✓ Clean C([C@H](C(=O)O)O)C(=O)O
NH4 P0A2K1 18.0 Da LogP 0.38 TPSA 36.5 ✓ Ro5 ✓ Clean [NH4+]
NHP P0A2K1 261.3 Da LogP 2.32 TPSA 83.6 ✓ Ro5 ✓ Clean c1ccc(c(c1)N)SCCCCP(=O)(O)O
P1T P9WFX9 318.2 Da LogP 0.39 TPSA 149.2 ✓ Ro5 ✓ Clean Cc1c(c(c(cn1)COP(=O)(O)O)CNC(=C)C(=O)O)O
PG5 P0A2K1 178.2 Da LogP 0.31 TPSA 36.9 ✓ Ro5 ✓ Clean COCCOCCOCCOC
PLR Q97TX6 233.2 Da LogP 1.01 TPSA 99.9 ✓ Ro5 ✓ Clean Cc1c(cnc(c1O)C)COP(=O)(O)O
PLS P0A2K1 336.2 Da LogP -0.76 TPSA 169.4 1 viol. ✓ Clean Cc1c(c(c(cn1)COP(=O)(O)O)CN[C@@H](CO)C(=O)O)O
PLT P0A2K1 433.4 Da LogP 2.30 TPSA 165.3 ✓ Ro5 ✓ Clean Cc1c(c(c(cn1)COP(=O)(O)O)\C=N\[C@@H](Cc2c[nH]c3…
PZJ P9WFX9 330.8 Da LogP 0.62 TPSA 60.9 ✓ Ro5 ✓ Clean c1ccc(c(c1)N2CCN(CC2)[C@H]3CS(=O)(=O)C[C@@H]3O)…
PZV P9WFX9 334.4 Da LogP 1.94 TPSA 66.5 ✓ Ro5 ✓ Clean CNS(=O)(=O)c1ccc2c(c1)CCN2C(=O)c3ccccc3F
SEP Q97TX6 185.1 Da LogP -1.49 TPSA 130.1 ✓ Ro5 ✓ Clean C([C@@H](C(=O)O)N)OP(=O)(O)O
V41 P0A2K1 205.2 Da LogP 0.56 TPSA 117.7 ✓ Ro5 Alert [H]/N=C(/[C@H](C(=O)N)/N=N/c1ccccc1)\N

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.