Protein target profile

VK055_3890

dihydropteroate synthase

Genome: KpATCC43816 Gene: folP AIK82440.1 3D evidence: Experimental + ColabFold model Metabolism 1 reaction UniProt A6TEJ6
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Length 265
Pocket druggability 0.307
Metabolic reactions 1
Chokepoint Yes
Direct ligand evidence 0 124 total records
Functional annotation 0 EC 4 GO
Target summary

Strong target candidate with converging metabolic, structural and chemical evidence.

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

Main supporting evidence

Metabolic bottleneck Catalyzes a reaction that is the only producer or consumer of a metabolite in the imported metabolic model. Experimental structure available At least one PDB experimental structure is loaded, not just a predicted model - stronger structural coverage than AlphaFold/ColabFold alone. Central metabolic position More central than 91.0% of genes in this genome. No isoenzyme backup detected Imported GPR rules do not show an alternative enzyme for the catalyzed reaction set. Review the complete evidence below

Risks to review

Microbiome similarity 219 of 4744 screened genomes (4.6%) have a significant similarity hit. Weak predicted binding pocket FPocket selected-pocket score 0.31. Weak second pocket-predictor signal P2Rank predicted binding-site probability 0.42.

Evidence coverage

Core evidence streams are available for this target.
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
No hit
Gut microbiome similarity
4.6% of screened genomes Lower prevalence suggests narrower overlap with the screened gut microbiome.

Essentiality

Essential (DEG)
Y
DEG identity (%)
89.434 Higher values support similarity to known essential genes.
DEG E-value
3.8400000000000004e-179 Smaller values mean stronger essential-gene similarity.

Localization

Localization
Cytoplasmic

Structure confidence

ColabFold pLDDT
94.93 0-100 confidence; >70 supports local structural interpretation.

Binding-site evidence

PDB experimental structure

The selected pocket score is the FPocket value used for ranking after applying the curated structure priority. It estimates small-molecule pocket quality; it is not experimental binding evidence. The 3D viewer may show a different loaded structure, so visible pockets can differ.

FPocket 0.307
Structure 5UMG
Pocket Pocket 3
P2Rank 0.418
Structure 5UMG
Pocket Pocket 1
ColabFold model
FPocket 0.952 · Pocket 2
P2Rank 0.875 · Pocket 1
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 219 / 4744 genomes with a hit
Prevalence 4.6%

Cross-references

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

Sequence

UniProt A6TEJ6

Structure

PDB 5UMG

Chemistry

ChEMBL CHEMBL158543 ChEMBL CHEMBL159139 ChEMBL CHEMBL159048 ChEMBL CHEMBL422884 ChEMBL CHEMBL1109 ChEMBL CHEMBL1191 ChEMBL CHEMBL1200321 ChEMBL CHEMBL1200351 ChEMBL CHEMBL1200359 ChEMBL CHEMBL1200910 ChEMBL CHEMBL1201161 ChEMBL CHEMBL1382627 ChEMBL CHEMBL1525826 ChEMBL CHEMBL1723241 ChEMBL CHEMBL2107253 ChEMBL CHEMBL268869 ChEMBL CHEMBL438 ChEMBL CHEMBL439 ChEMBL CHEMBL446 ChEMBL CHEMBL453 ChEMBL CHEMBL455 ChEMBL CHEMBL58061 ChEMBL CHEMBL62193 ChEMBL SFY ChEMBL YTZ

Pathways

KEGG R03067 BioCyc H2PTEROATESYNTH-RXN

Metabolic context

Reactions catalyzed, pathway membership, and centrality in the genome-scale metabolic network.

Explore metabolic network

Attractive metabolic target: catalyzes a producing & consuming chokepoint reaction in Folate biosynthesis, no isoenzyme backup detected, more central than 91.0% of genes in this genome, no human homolog detected.

Relative network centrality 91.0% more central than 91.0% of genes in this genome
Chokepoint Chokepoint gene
Pathways
Folate biosynthesis
Catalyzed reaction

1 reaction mapped to this gene in the metabolic model. Open the full network to see each one, with substrates/products and the reaction-reaction map.

Imported from KpATCC43816.sbml · 2026-07-09

Sequence

Primary amino-acid sequence viewer.

MGILNVTPDSFSDGGAHNSLIEAVKHANLMINAGATIIDIGGESTRPGAAEVSVEEELARVIPVVEAIAQRFEVWISVDTSKAEVIRQSARAGAHIINDIRSLTEPGALQAAAETGLPVCLMHMQGQPKTMQEAPKYEDVFADVERFFNEHIVRCEQAGIAKEKLLLDPGFGFGKNLSHNYQLLARLGEFHHFGLPLLVGMSRKSMVGQLLNVGPSERLNGSLACAVIAAMQGAQIIRVHDVKETVEALRVVEATLAAKGKKRYE

Functional annotations

Enzyme classification and Gene Ontology terms linked to this protein.

4 GO

Gene Ontology (GO)

4
  • GO:0044237 OBSOLETE. The chemical reactions and pathways by which individual cells transform chemical substances.
  • GO:0004156 Catalysis of the reaction: 2-amino-4-hydroxy-6-hydroxymethyl-7,8-dihydropteridine diphosphate + 4-aminobenzoate = diphosphate + dihydropteroate.
  • GO:0042558 The chemical reactions and pathways involving any compound containing pteridine (pyrazino(2,3-dipyrimidine)), e.g. pteroic acid, xanthopterin and folic acid.
  • GO:0009396 The chemical reactions and pathways resulting in the formation of folic acid and its derivatives.

Sequence domains and features

Domain and signature matches imported from InterPro and related databases.

17 records
Show feature table
Start End DB Term Name
1 265 Gene3D G3DSA:3.20.20.20 -
1 265 InterPro IPR011005 Dihydropteroate synthase-like
1 261 FunFam G3DSA:3.20.20.20:FF:000004 Dihydropteroate synthase
1 256 PANTHER PTHR20941 FOLATE SYNTHESIS PROTEINS
1 256 InterPro IPR045031 Dihydropteroate synthase
1 256 SUPERFAMILY SSF51717 Dihydropteroate synthetase-like
1 256 InterPro IPR011005 Dihydropteroate synthase-like
1 240 Pfam PF00809 Pterin binding enzyme
1 240 InterPro IPR000489 Pterin-binding domain
34 47 ProSitePatterns PS00793 Dihydropteroate synthase signature 2.
34 47 InterPro IPR000489 Pterin-binding domain
1 250 ProSiteProfiles PS50972 Pterin-binding domain profile.
1 250 InterPro IPR000489 Pterin-binding domain
1 253 CDD cd00739 DHPS
1 253 InterPro IPR006390 Dihydropteroate synthase domain
1 254 NCBIfam TIGR01496 dihydropteroate synthase
1 254 InterPro IPR006390 Dihydropteroate synthase 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.

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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 · FPocket

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

Site 1 FPocket #3
0.307
Likely same site as P2Rank 3 7.6 Å 3 shared residues 60% of smaller site
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Surrounding area

Binding pockets · P2Rank

Probability: high ≥ 0.5 · medium 0.2–0.49 · low < 0.2

Site 1 P2Rank #1
0.418
Show in viewer
Surrounding area
Site 2 P2Rank #2
0.009
Show in viewer
Surrounding area
Site 3 P2Rank #3
0.003
Likely same site as FPocket 3 7.6 Å 3 shared residues 60% of smaller site
Show in viewer
Surrounding area
All structural evidence 1 experimental · 1 predicted

Structural evidence

1 + 1

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
PDB 5UMG
X-ray — A —
PDBe RCSB PDBj File
Viewing
ColabFold VK055_3890
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.

124 records
Chemistry signal

Structural and bioactivity evidence are both available for this target.

Direct evidence 0 same-protein records
Transferred evidence 74 records from similar proteins
Structural ligands 49 0 loaded crystals
Measured bioactivity 25 direct and transferred ChEMBL records
Proposed compounds 50 similarity-based ZINC candidates
Best available ligand signal
08D PDB via homolog 253.3 Da · LogP 1.37 · TPSA 98.2 Open detail RCSB PDB
0HY PDB via homolog Detail RCSB PDB
0J2 PDB via homolog Detail RCSB PDB
0J4 PDB via homolog Detail RCSB PDB
0J5 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
08D RCSB PDB
3TZF
A0A2S9PLG4 253.3 Da LogP 1.37 TPSA 98.2 ✓ Ro5 ✓ Clean Cc1cc(no1)NS(=O)(=O)c2ccc(cc2)N
0HY RCSB PDB
4D8A
Q81VW8 279.3 Da LogP -0.74 TPSA 143.8 ✓ Ro5 ✓ Clean C[C@H](CC(=O)OC)C1=NNC2=C(C1=O)C(=O)NC(=N2)N
0J2 RCSB PDB
4D8Z
Q81VW8 265.2 Da LogP -0.83 TPSA 154.8 ✓ Ro5 ✓ Clean C[C@H](CC(=O)O)C1=NNC2=C(C1=O)C(=O)NC(=N2)N
0J4 RCSB PDB
4DAF
Q81VW8 251.2 Da LogP -1.22 TPSA 154.8 ✓ Ro5 ✓ Clean C[C@H](C1=NNC2=C(C1=O)C(=O)NC(=N2)N)C(=O)O
0J5 RCSB PDB
4DAI
Q81VW8 237.2 Da LogP -1.78 TPSA 154.8 ✓ Ro5 ✓ Clean C(C1=NNC2=C(C1=O)C(=O)NC(=N2)N)C(=O)O
22D RCSB PDB
6OFW
D2UDM3 312.3 Da LogP 0.61 TPSA 146.9 ✓ Ro5 ✓ Clean c1cc(ccc1C(=O)O)NCc2cnc3c(n2)C(=O)NC(=N3)N
2O6 RCSB PDB
4NHV
Q81VW8 202.1 Da LogP 2.43 TPSA 52.0 ✓ Ro5 ✓ Clean c1cc2c(cc1C(F)(F)F)c(no2)N
2O8 RCSB PDB
4NIL
Q81VW8 221.2 Da LogP 2.40 TPSA 43.1 ✓ Ro5 ✓ Clean c1cc(ccc1C(=O)N)SC(F)(F)F
2PH RCSB PDB
1AJ2
P0AC13 355.1 Da LogP -0.92 TPSA 209.4 1 viol. ✓ Clean C1C(=NC2=C(N1)N=C(NC2=O)N)CO[P@@](=O)(O)OP(=O)(…
5RU RCSB PDB
5U12
P0AC13 291.3 Da LogP 1.66 TPSA 100.5 ✓ Ro5 ✓ Clean c1ccc(c(c1)CSc2[nH]c3c(n2)C(=O)NC(=N3)N)F
680 RCSB PDB
1TX2
Q81VW8 185.1 Da LogP -0.70 TPSA 126.9 ✓ Ro5 ✓ Clean CNC1=C(C(=O)NC(=N1)N)[N+](=O)[O-]
6DH RCSB PDB
4NIR
Q81VW8 244.2 Da LogP 2.51 TPSA 48.9 ✓ Ro5 ✓ Clean c1cc2c(cc1C(F)(F)F)[nH]c(n2)CCCO
6GU RCSB PDB
6Q62
D2UDM3 169.6 Da LogP 0.59 TPSA 80.5 ✓ Ro5 ✓ Clean c1[nH]c2c(n1)c(nc(n2)N)Cl
6MB RCSB PDB
5JQ9
A0A2S9PLG4 442.5 Da LogP 1.31 TPSA 181.8 ✓ Ro5 ✓ Clean Cc1c(noc1NS(=O)(=O)c2ccc(cc2)NCc3cnc4c(n3)C(=O)…
78H RCSB PDB
3TYA
Q81VW8 314.3 Da LogP 0.66 TPSA 145.5 ✓ Ro5 ✓ Clean c1cc(ccc1C(=O)O)NCC2=NC3=C(NC2)N=C(NC3=O)N
7PJ RCSB PDB
5U0Y
P0AC13 241.2 Da LogP -0.59 TPSA 137.7 ✓ Ro5 ✓ Clean C(C(=O)O)Sc1[nH]c2c(n1)C(=O)NC(=N2)N
7PM RCSB PDB
5U0Z
P0AC13 317.3 Da LogP 1.15 TPSA 137.7 ✓ Ro5 ✓ Clean c1ccc(cc1)[C@H](C(=O)O)Sc2[nH]c3c(n2)C(=O)NC(=N…
7PS RCSB PDB
5U11
P0AC13 254.3 Da LogP -0.93 TPSA 129.5 ✓ Ro5 ✓ Clean CNC(=O)CSc1[nH]c2c(n1)C(=O)NC(=N2)N
7PV RCSB PDB
5U14
P0AC13 366.4 Da LogP 0.21 TPSA 160.6 ✓ Ro5 ✓ Clean c1cc(ccc1CCSc2[nH]c3c(n2)C(=O)NC(=N3)N)S(=O)(=O…
7VJ RCSB PDB
5U0V
P0AC13 169.1 Da LogP -0.21 TPSA 113.2 ✓ Ro5 ✓ Clean CNC1=C(C(=O)NC(=N1)N)N=O
8Y4 RCSB PDB
5V79
P0AC13 330.4 Da LogP 0.97 TPSA 118.7 ✓ Ro5 ✓ Clean Cn1c2c(nc1SCC(=O)Nc3ccccc3)C(=O)NC(=N2)N
8Y7 RCSB PDB
5V7A
P0AC13 255.3 Da LogP -0.58 TPSA 126.9 ✓ Ro5 ✓ Clean Cn1c2c(nc1SCC(=O)O)C(=O)NC(=N2)N
9MG RCSB PDB
5U0W
P0AC13 165.2 Da LogP -0.35 TPSA 89.8 ✓ Ro5 ✓ Clean Cn1cnc2c1nc(nc2O)N
B52 RCSB PDB
3H21
Q81VW8 265.2 Da LogP -1.21 TPSA 144.0 ✓ Ro5 ✓ Clean C[C@H](C1=NN(C2=C(C1=O)C(=O)NC(=N2)N)C)C(=O)O
B53 RCSB PDB
3H22
Q81VW8 155.1 Da LogP -0.67 TPSA 127.2 ✓ Ro5 ✓ Clean C1(=C(N=C(NC1=O)N)N)N=O
B54 RCSB PDB
3H23
Q81VW8 333.3 Da LogP 1.33 TPSA 159.8 ✓ Ro5 ✓ Clean c1cc(ccc1C(=O)O)OCCCNC2=C(C(=O)NC(=N2)N)N=O
B55 RCSB PDB
3H24
Q81VW8 183.2 Da LogP -0.48 TPSA 100.5 ✓ Ro5 ✓ Clean c12c([nH]c(n1)S)N=C(NC2=O)N
B56 RCSB PDB
3H26
Q81VW8 223.2 Da LogP -1.04 TPSA 124.7 ✓ Ro5 ✓ Clean CN1CC(=NC2=C1N=C(NC2=O)N)C(=O)O
B57 RCSB PDB
3H2A
Q81VW8 171.1 Da LogP -1.16 TPSA 140.9 ✓ Ro5 ✓ Clean C1(=C(N=C(NC1=O)N)N)[N+](=O)[O-]
B58 RCSB PDB
3H2C
Q81VW8 150.1 Da LogP -0.48 TPSA 106.5 ✓ Ro5 ✓ Clean c1[nH]c2c(n1)c(nnc2N)N
B59 RCSB PDB
3H2E
Q81VW8 236.2 Da LogP -1.87 TPSA 106.8 ✓ Ro5 ✓ Clean CN1C2=C(C(=O)N(C1=O)C)N=C(C(=O)N2)C=O
B60 RCSB PDB
3H2F
Q81VW8 179.2 Da LogP -0.50 TPSA 87.4 ✓ Ro5 ✓ Clean CN1CC=NC2=C1N=C(NC2=O)N
B61 RCSB PDB
3H2M
Q81VW8 251.3 Da LogP 0.04 TPSA 107.6 ✓ Ro5 ✓ Clean CC(C)(CC1=NC2=C(N=C(NC2=O)N)N(C1)C)O
B62 RCSB PDB
3H2N
Q81VW8 181.2 Da LogP -0.42 TPSA 95.8 ✓ Ro5 ✓ Clean C[C@@H]1CNC2=C(N1)C(=O)NC(=N2)N
B63 RCSB PDB
3H2O
Q81VW8 328.3 Da LogP 1.05 TPSA 145.5 ✓ Ro5 ✓ Clean c1cc(ccc1C(=O)O)NCCC2=NC3=C(NC2)N=C(NC3=O)N
HH2 RCSB PDB
1TWW
Q81VW8 353.1 Da LogP -0.98 TPSA 210.8 ✓ Ro5 ✓ Clean c1c(nc2c(n1)N=C(NC2=O)N)CO[P@](=O)(O)OP(=O)(O)O
ICB RCSB PDB
6Q62
D2UDM3 161.2 Da LogP 1.87 TPSA 53.1 ✓ Ro5 ✓ Clean c1ccc2c(c1)cc([nH]2)C(=O)O
PAB RCSB PDB
6DAY
D2UDM3 137.1 Da LogP 0.97 TPSA 63.3 ✓ Ro5 ✓ Clean c1cc(ccc1C(=O)O)N
PH2 RCSB PDB
1AJ0
P0AC13 195.2 Da LogP -1.16 TPSA 116.4 ✓ Ro5 ✓ Clean C1C(=NC2=C(N1)N=C(NC2=O)N)CO
PHB RCSB PDB
3TYB
Q81VW8 138.1 Da LogP 1.09 TPSA 57.5 ✓ Ro5 ✓ Clean c1cc(ccc1C(=O)O)O
PMM RCSB PDB
1TWZ
Q81VW8 273.1 Da LogP -1.10 TPSA 164.3 ✓ Ro5 ✓ Clean c1c(nc2c(n1)N=C(NC2=O)N)COP(=O)(O)O
POP RCSB PDB
3TYD
Q81VW8 176.0 Da LogP -2.08 TPSA 129.9 ✓ Ro5 ✓ Clean O[P@@](=O)([O-])O[P@@](=O)(O)[O-]
SAN RCSB PDB
1AJ0
P0AC13 172.2 Da LogP -0.08 TPSA 86.2 ✓ Ro5 ✓ Clean c1cc(ccc1N)S(=O)(=O)N
XHP RCSB PDB
3TYB
Q81VW8 177.2 Da LogP -1.88 TPSA 96.5 ✓ Ro5 ✓ Clean C=C1CN=C2C(=N1)C(=O)NC(=N2)N
XTZ RCSB PDB
3TYE
Q81VW8 432.5 Da LogP 1.22 TPSA 167.2 ✓ Ro5 ✓ Clean c1cc(ccc1NCC2=NC3=C(NC2)N=C(NC3=O)N)S(=O)(=O)Nc…
YH5 RCSB PDB
5U13
P0AC13 331.4 Da LogP 1.21 TPSA 126.8 ✓ Ro5 ✓ Clean COc1ccc(cc1)C(=O)CSc2[nH]c3c(n2)C(=O)NC(=N3)N
Z13 RCSB PDB
4NL1
Q81VW8 331.3 Da LogP 5.34 TPSA 12.4 1 viol. ✓ Clean c1cc(ccc1CN=Cc2ccc(cc2)C(F)(F)F)C(F)(F)F
Z17 RCSB PDB
4D9P
Q81VW8 279.3 Da LogP -0.82 TPSA 144.0 ✓ Ro5 ✓ Clean C[C@H](CC(=O)O)C1=NN(C2=C(C1=O)C(=O)NC(=N2)N)C
Z25 RCSB PDB
4DB7
Q81VW8 251.2 Da LogP -1.39 TPSA 154.8 ✓ Ro5 ✓ Clean C(CC(=O)O)C1=NNC2=C(C1=O)C(=O)NC(=N2)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.