Protein profile

KP13_02393

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

Genome: KpKP13

Gene: queD AHE42964.1 Structure source: AlphaFold + ColabFold UniProt A0A0H3H223

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Amino acids 121

Annotations 4

Features 13

PDB binders 3

Druggability 0.079

Overview

Basic information about this protein and its source genome.

Accession: KP13_02393
Assembly: Klebsiella pneumoniae subsp. pneumoniae Kp13, complete sequence
Gene: queD AHE42964.1
Status: annotated
Amino acids: 121
Structure source: AlphaFold + ColabFold

4.-.-.-

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.

Target profile

Computed evidence for target prioritization.

Human off-target: hit
Human identity (%): 37.113
Human E-value: 9.67e-12
Gut microbiome off-target: hit
Essential (DEG): Y
DEG identity (%): 80.165
DEG E-value: 2.94e-75
Localization: Cytoplasmic
ColabFold pLDDT: 97.47

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 0.079

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

Normalized 0.029

Sequence

Primary amino-acid sequence viewer.

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 Features

Domain/signature hits 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; predicted models typically cover the full protein.

Loading 3D structure...

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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_A0A0H3H223	AlphaFold	—	—	full sequence	—	Viewing
ColabFold KP13_02393	ColabFold	—	—	full sequence	—	Loaded

Pocket details FPocket · P2Rank — toggle visibility and zoom from here, or open full viewer

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				0.83	0.003

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

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.

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	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	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	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	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	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	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	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	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	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	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	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	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	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	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	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	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	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	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	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	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	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	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	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	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	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	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	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	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	0.533	207.2 Da LogP -1.17 TPSA 117.8	✓ Ro5	✓ Clean	`Nc1nc2ncc(CCO)nc2c(=O)[nH]1`
ZINC5807319	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	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	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	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	0.511	211.6 Da LogP 0.03 TPSA 97.5	✓ Ro5	✓ Clean	`Nc1nc2ncc(CCl)nc2c(=O)[nH]1`
ZINC3869856	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	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	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.