Protein target profile

KP13_02393

6-carboxy-5,6,7,8-tetrahydropterin synthase

Genome: KpKP13 Gene: queD AHE42964.1 3D evidence: AlphaFold DB model + ColabFold model UniProt A0A0H3H223

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Length 121

Pocket druggability 0.079

Direct ligand evidence 0 37 total records

Functional annotation 1 EC 3 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 (%): 37.113 Lower values reduce human off-target concern.
Human E-value: 9.67e-12
Gut microbiome similarity: 2.9% of screened genomes Lower prevalence suggests narrower overlap with the screened gut microbiome.

Essentiality

Essential (DEG): Y
DEG identity (%): 80.165 Higher values support similarity to known essential genes.
DEG E-value: 2.94e-75 Smaller values mean stronger essential-gene similarity.

Localization

Localization: Cytoplasmic

Structure confidence

ColabFold pLDDT: 97.47 0-100 confidence; >70 supports local structural interpretation.

Binding-site evidence

AlphaFold DB / UniProt model

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 0.079

Structure A0A0H3H223

Pocket Pocket 1

P2Rank 0.037

Structure A0A0H3H223

Pocket Pocket 1

ColabFold model

FPocket 0.128 · Pocket 3

P2Rank 0.144 · Pocket 1

Core conservation Accessory gene

Roary core

CoreCruncher accessory

Gut microbiome 137 / 4744 genomes with a hit

Prevalence 2.9%

Cross-references

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

Sequence

UniProt A0A0H3H223

Sequence

Primary amino-acid sequence viewer.

MMSTTLFKDFTFEAAHHLPHVPEGHKCGRLHGHSFMVRLEITGEVDPHTGWIMDFAELKAAFKPTYDRLDHYYLNDIPGLENPTSEVLAKWIWDEMKPRVPLLSAVMVKETCTAGCVYRGE

Functional annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 3 GO

Enzyme Commission (EC)

4.-.-.-

Gene Ontology (GO)

GO:0070497 Catalysis of the reaction: 7,8-dihydroneopterin 3'-triphosphate + H2O = 6-carboxy-5,6,7,8-tetrahydropterin + triphosphate + acetaldehyde + 2 H+.
GO:0046872 Binding to a metal ion.
GO:0008616 The chemical reactions and pathways resulting in the formation of queuosines, a series of nucleosides found in position 34 of tRNA and having an additional pentenyl ring added via an NH group to the methyl group of 7-methylguanosine. The pentenyl ring may carry other substituents. The wobble nucleoside of the tRNA sequence (position 34) corresponds to the first position of the anticodon.

Sequence domains and features

Domain and signature matches imported from InterPro and related databases.

13 records

Show feature table

Start	End	DB	Term	Name
4	121	NCBIfam	TIGR00039	6-pyruvoyl tetrahydropterin synthase/QueD family protein
4	121	InterPro	IPR007115	6-pyruvoyl tetrahydropterin synthase/QueD family
1	121	PIRSF	PIRSF006113	PTP_synth
1	121	InterPro	IPR007115	6-pyruvoyl tetrahydropterin synthase/QueD family
6	97	NCBIfam	TIGR03367	6-carboxytetrahydropterin synthase QueD
1	120	SUPERFAMILY	SSF55620	Tetrahydrobiopterin biosynthesis enzymes-like
3	121	PANTHER	PTHR12589	PYRUVOYL TETRAHYDROBIOPTERIN SYNTHASE
3	121	InterPro	IPR007115	6-pyruvoyl tetrahydropterin synthase/QueD family
2	121	FunFam	G3DSA:3.30.479.10:FF:000001	6-carboxy-5,6,7,8-tetrahydropterin synthase
6	121	Pfam	PF01242	6-pyruvoyl tetrahydropterin synthase
6	121	InterPro	IPR007115	6-pyruvoyl tetrahydropterin synthase/QueD family
1	121	Gene3D	G3DSA:3.30.479.10	-
1	121	InterPro	IPR038418	6-pyruvoyl tetrahydropterin synthase/QueD superfamily

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

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

Site 1 P2Rank #1

0.037

Show in viewer

Surrounding area

Site 2 P2Rank #2

0.014

Show in viewer

Surrounding area

Residue sets

UniProt: Active site:110-110 Charge relay system

UniProt: Active site:27-27 Proton acceptor

UniProt: Active site:71-71 Charge relay system

UniProt: Binding site:16-16

UniProt: Binding site:31-31

UniProt: Binding site:33-33

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_A0A0H3H223	AlphaFold DB	—	—	full sequence	—	Viewing
ColabFold KP13_02393	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.

37 records

Chemistry signal

Structural ligand evidence is available for this target.

Direct evidence 0 same-protein records

Transferred evidence 3 records from similar proteins

Structural ligands 3 0 loaded crystals

Measured bioactivity 0 direct and transferred ChEMBL records

Proposed compounds 34 similarity-based ZINC candidates

Best available ligand signal

2K8 PDB via homolog 211.2 Da · LogP -1.36 · TPSA 133.1 Open detail RCSB PDB

BIO PDB via homolog Detail RCSB PDB

ZSP PDB via homolog Detail RCSB PDB

ZINC103562712 ZINC proposed compound · Tanimoto 1.000 Detail ZINC

ZINC17129255 ZINC proposed compound · Tanimoto 1.000 Detail ZINC

Highest-confidence structural evidence: ligands co-crystallized with this exact protein. If the source PDB is loaded in Target, use Open crystal to inspect it in the structure viewer.

No PDB structure with a co-crystallized ligand found for this exact protein.

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.

Ligand	Source crystal	UniProt (homolog)	MW · LogP · TPSA	Lipinski	PAINS	SMILES
2K8 RCSB PDB	4NTM	P65870	211.2 Da LogP -1.36 TPSA 133.1	✓ Ro5	✓ Clean	`C1[C@@H](NC2=C(N1)N=C(NC2=O)N)C(=O)O`
BIO RCSB PDB	1Y13	C6KTB6	237.2 Da LogP -1.29 TPSA 138.0	✓ Ro5	✓ Clean	`C[C@H]([C@H](c1cnc2c(n1)C(=O)NC(=N2)N)O)O`
ZSP RCSB PDB	4NTK	P65870	237.2 Da LogP 0.20 TPSA 136.6	✓ Ro5	✓ Clean	`C/C(=C(\C1=NC2=C(NC1)N=C(NC2=O)N)/O)/O`

Experimental bioactivity from ChEMBL measured directly on this protein. Score = pchembl (−log Ki/IC₅₀; higher = more potent).

No ChEMBL bioactivity data found for this exact protein.

Bioactivity inferred from similar proteins in ChEMBL. Score = pchembl (−log Ki/IC₅₀; higher = more potent).

No ChEMBL hits found through similar proteins.

Proposed virtual-screening candidates from ZINC. Score = Tanimoto similarity to a known binder (0–1; higher = more similar).

Ligand	Tanimoto	MW · LogP · TPSA	Lipinski	PAINS	SMILES
ZINC103562712 ZINC	1.000	237.2 Da LogP 0.20 TPSA 136.6	✓ Ro5	✓ Clean	`C/C(O)=C(/O)C1=Nc2c(nc(N)[nH]c2=O)NC1`
ZINC17129255 ZINC	1.000	237.2 Da LogP -1.29 TPSA 138.0	✓ Ro5	✓ Clean	`C[C@@H](O)[C@@H](O)c1cnc2nc(N)[nH]c(=O)c2n1`
ZINC17129257 ZINC	1.000	237.2 Da LogP -1.29 TPSA 138.0	✓ Ro5	✓ Clean	`C[C@H](O)[C@@H](O)c1cnc2nc(N)[nH]c(=O)c2n1`
ZINC17129259 ZINC	1.000	237.2 Da LogP -1.29 TPSA 138.0	✓ Ro5	✓ Clean	`C[C@@H](O)[C@H](O)c1cnc2nc(N)[nH]c(=O)c2n1`
ZINC18275062 ZINC	1.000	237.2 Da LogP -1.29 TPSA 138.0	✓ Ro5	✓ Clean	`C[C@H](O)[C@H](O)c1cnc2nc(N)[nH]c(=O)c2n1`
ZINC7998083 ZINC	0.850	267.2 Da LogP -1.93 TPSA 158.2	✓ Ro5	✓ Clean	`C[C@H](O)[C@H](O)[C@@H](O)c1cnc2nc(N)[nH]c(=O)c…`
ZINC8568890 ZINC	0.850	267.2 Da LogP -1.93 TPSA 158.2	✓ Ro5	✓ Clean	`C[C@H](O)[C@H](O)[C@H](O)c1cnc2nc(N)[nH]c(=O)c2…`
ZINC8602624 ZINC	0.850	267.2 Da LogP -1.93 TPSA 158.2	✓ Ro5	✓ Clean	`C[C@H](O)[C@@H](O)[C@H](O)c1cnc2nc(N)[nH]c(=O)c…`
ZINC14420733 ZINC	0.800	237.2 Da LogP -1.29 TPSA 138.0	✓ Ro5	✓ Clean	`C[C@@H](O)[C@@H](O)c1cnc2c(=O)[nH]c(N)nc2n1`
ZINC17860887 ZINC	0.800	237.2 Da LogP -1.29 TPSA 138.0	✓ Ro5	✓ Clean	`C[C@H](O)[C@H](O)c1cnc2c(=O)[nH]c(N)nc2n1`
ZINC17994680 ZINC	0.800	237.2 Da LogP -1.29 TPSA 138.0	✓ Ro5	✓ Clean	`C[C@@H](O)[C@H](O)c1cnc2c(=O)[nH]c(N)nc2n1`
ZINC18036401 ZINC	0.800	237.2 Da LogP -1.29 TPSA 138.0	✓ Ro5	✓ Clean	`C[C@H](O)[C@@H](O)c1cnc2c(=O)[nH]c(N)nc2n1`
ZINC12428336 ZINC	0.738	253.2 Da LogP -2.32 TPSA 158.2	✓ Ro5	✓ Clean	`Nc1nc2ncc([C@H](O)[C@H](O)CO)nc2c(=O)[nH]1`
ZINC17176122 ZINC	0.738	253.2 Da LogP -2.32 TPSA 158.2	✓ Ro5	✓ Clean	`Nc1nc2ncc([C@@H](O)[C@@H](O)CO)nc2c(=O)[nH]1`
ZINC17176123 ZINC	0.738	253.2 Da LogP -2.32 TPSA 158.2	✓ Ro5	✓ Clean	`Nc1nc2ncc([C@H](O)[C@@H](O)CO)nc2c(=O)[nH]1`
ZINC18169010 ZINC	0.738	253.2 Da LogP -2.32 TPSA 158.2	✓ Ro5	✓ Clean	`Nc1nc2ncc([C@@H](O)[C@H](O)CO)nc2c(=O)[nH]1`
ZINC1560411723 ZINC	0.605	237.2 Da LogP 0.61 TPSA 136.9	✓ Ro5	✓ Clean	`C/C(O)=C(\O)C1=Nc2c(O)nc(N)nc2NC1`
ZINC13585233 ZINC	0.578	241.3 Da LogP -1.70 TPSA 136.3	1 viol.	✓ Clean	`C[C@H](O)[C@H](O)[C@H]1CNc2nc(N)[nH]c(=O)c2N1`
ZINC13815072 ZINC	0.578	241.3 Da LogP -1.70 TPSA 136.3	1 viol.	✓ Clean	`C[C@@H](O)[C@@H](O)[C@H]1CNc2nc(N)[nH]c(=O)c2N1`
ZINC13815079 ZINC	0.578	241.3 Da LogP -1.70 TPSA 136.3	1 viol.	✓ Clean	`C[C@@H](O)[C@H](O)[C@H]1CNc2nc(N)[nH]c(=O)c2N1`
ZINC18059633 ZINC	0.578	241.3 Da LogP -1.70 TPSA 136.3	1 viol.	✓ Clean	`C[C@H](O)[C@@H](O)[C@H]1CNc2nc(N)[nH]c(=O)c2N1`
ZINC4228257 ZINC	0.578	241.3 Da LogP -1.70 TPSA 136.3	1 viol.	✓ Clean	`C[C@H](O)[C@@H](O)[C@@H]1CNc2nc(N)[nH]c(=O)c2N1`
ZINC18181336 ZINC	0.553	239.2 Da LogP -1.41 TPSA 136.6	✓ Ro5	✓ Clean	`C[C@H](O)[C@H](O)C1=Nc2c(nc(N)[nH]c2=O)NC1`
ZINC95617488 ZINC	0.553	239.2 Da LogP -1.41 TPSA 136.6	✓ Ro5	✓ Clean	`C[C@@H](O)[C@@H](O)C1=Nc2c(nc(N)[nH]c2=O)NC1`
ZINC17703936 ZINC	0.542	267.2 Da LogP -1.93 TPSA 158.2	✓ Ro5	✓ Clean	`C[C@H](O)[C@@H](O)[C@@H](O)c1cnc2[nH]c(N)nc(=O)…`
ZINC17429362 ZINC	0.533	207.2 Da LogP -1.17 TPSA 117.8	✓ Ro5	✓ Clean	`Nc1nc2ncc(CCO)nc2c(=O)[nH]1`
ZINC5807319 ZINC	0.520	284.3 Da LogP -1.18 TPSA 132.2	✓ Ro5	✓ Clean	`CSc1nc2ncc([C@H](O)[C@H](O)CO)nc2c(=O)[nH]1`
ZINC5807320 ZINC	0.520	284.3 Da LogP -1.18 TPSA 132.2	✓ Ro5	✓ Clean	`CSc1nc2ncc([C@H](O)[C@@H](O)CO)nc2c(=O)[nH]1`
ZINC5807321 ZINC	0.520	284.3 Da LogP -1.18 TPSA 132.2	✓ Ro5	✓ Clean	`CSc1nc2ncc([C@@H](O)[C@H](O)CO)nc2c(=O)[nH]1`
ZINC5807322 ZINC	0.520	284.3 Da LogP -1.18 TPSA 132.2	✓ Ro5	✓ Clean	`CSc1nc2ncc([C@@H](O)[C@@H](O)CO)nc2c(=O)[nH]1`
ZINC142664839 ZINC	0.511	211.6 Da LogP 0.03 TPSA 97.5	✓ Ro5	✓ Clean	`Nc1nc2ncc(CCl)nc2c(=O)[nH]1`
ZINC3869856 ZINC	0.510	255.2 Da LogP -2.44 TPSA 156.8	1 viol.	✓ Clean	`Nc1nc2c(c(=O)[nH]1)N=C([C@@H](O)[C@H](O)CO)CN2`
ZINC4096578 ZINC	0.510	255.2 Da LogP -2.44 TPSA 156.8	1 viol.	✓ Clean	`Nc1nc2c(c(=O)[nH]1)N=C([C@H](O)[C@H](O)CO)CN2`
ZINC8664075 ZINC	0.509	330.3 Da LogP 0.76 TPSA 145.2	1 viol.	✓ Clean	`Nc1nc2c(c(=O)[nH]1)N[C@@H](CCNc1ccc(C(=O)O)cc1)…`

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.

KP13_02393

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

Main supporting evidence

Risks to review

Evidence gaps

Prioritization evidence

Off-target risk

Essentiality

Localization

Structure confidence

Binding-site evidence

Cross-references

Sequence

Sequence

Functional annotations

Enzyme Commission (EC)

Gene Ontology (GO)

Sequence domains and features

3D structure

Binding pockets · P2Rank

Binding pockets · P2Rank

Structural evidence

Ligand evidence