Protein profile

KP13_14111

3-dehydroquinate dehydratase

Genome: KpKP13

Gene: aroD ANJ86627.1 Structure source: AlphaFold + ColabFold UniProt A0A0H3GMI6

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Amino acids 251

Annotations 6

Features 15

PDB binders 18

Druggability 0.39

Overview

Basic information about this protein and its source genome.

Accession: KP13_14111
Assembly: Klebsiella pneumoniae subsp. pneumoniae Kp13, complete sequence
Gene: aroD ANJ86627.1
Status: annotated
Amino acids: 251
Structure source: AlphaFold + ColabFold

4.2.1.10

GO:0003855 Catalysis of the reaction: 3-dehydroquinate = 3-dehydroshikimate + H2O. GO:0046279 The chemical reactions and pathways resulting in the formation of 3,4-dihydroxybenzoate. GO:0008652 The chemical reactions and pathways resulting in the formation of amino acids, organic acids containing one or more amino substituents. GO:0009073 The chemical reactions and pathways resulting in the formation of aromatic amino acid family, amino acids with aromatic ring (phenylalanine, tyrosine, tryptophan). GO:0009423 The chemical reactions and pathways resulting in the formation of the unsymmetrical ether derived from phosphoenolpyruvate and 5-phosphoshikimic acid formed as an intermediate in the biosynthesis of aromatic amino acids and many other compounds.

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 (%): 56.504
DEG E-value: 9.62e-95
Localization: Cytoplasmic
ColabFold pLDDT: 95.95

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 0.39

Structure A0A0H3GMI6

Pocket Pocket 2

P2Rank 0.463

Structure A0A0H3GMI6

Pocket Pocket 1

ColabFold model

FPocket 0.498 · Pocket 1

P2Rank 0.47 · Pocket 1

Core conservation Conserved core gene

Roary core

CoreCruncher core

Gut microbiome 171 / 4744 genomes with a hit

Normalized 0.036

Sequence

Primary amino-acid sequence viewer.

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 5 GO

Enzyme Commission (EC)

4.2.1.10

Gene Ontology (GO)

GO:0003855 Catalysis of the reaction: 3-dehydroquinate = 3-dehydroshikimate + H2O.
GO:0046279 The chemical reactions and pathways resulting in the formation of 3,4-dihydroxybenzoate.
GO:0008652 The chemical reactions and pathways resulting in the formation of amino acids, organic acids containing one or more amino substituents.
GO:0009073 The chemical reactions and pathways resulting in the formation of aromatic amino acid family, amino acids with aromatic ring (phenylalanine, tyrosine, tryptophan).
GO:0009423 The chemical reactions and pathways resulting in the formation of the unsymmetrical ether derived from phosphoenolpyruvate and 5-phosphoshikimic acid formed as an intermediate in the biosynthesis of aromatic amino acids and many other compounds.

Sequence Features

Domain/signature hits from InterPro and related databases.

15 records

Show feature table

Start	End	DB	Term	Name
115	145	ProSitePatterns	PS01028	Dehydroquinase class I active site.
115	145	InterPro	IPR018508	3-dehydroquinate dehydratase, active site
19	246	NCBIfam	TIGR01093	type I 3-dehydroquinate dehydratase
19	246	InterPro	IPR001381	3-dehydroquinate dehydratase type I
18	249	CDD	cd00502	DHQase_I
18	249	InterPro	IPR001381	3-dehydroquinate dehydratase type I
18	250	Hamap	MF_00214	3-dehydroquinate dehydratase [aroD].
18	250	InterPro	IPR001381	3-dehydroquinate dehydratase type I
3	250	SUPERFAMILY	SSF51569	Aldolase
19	250	PANTHER	PTHR43699	3-DEHYDROQUINATE DEHYDRATASE
2	251	FunFam	G3DSA:3.20.20.70:FF:000047	3-dehydroquinate dehydratase
1	251	Gene3D	G3DSA:3.20.20.70	Aldolase class I
1	251	InterPro	IPR013785	Aldolase-type TIM barrel
20	246	Pfam	PF01487	Type I 3-dehydroquinase
20	246	InterPro	IPR001381	3-dehydroquinate dehydratase type I

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_A0A0H3GMI6	AlphaFold	—	—	full sequence	—	Viewing
ColabFold KP13_14111	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
2				0.39

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				7.05	0.365

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				0.498

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				7.98	0.424

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.

57 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
3DS	4GUG	P58687	172.1 Da LogP -1.31 TPSA 94.8	✓ Ro5	✓ Clean	`C1[C@H]([C@@H](C(=O)C=C1C(=O)O)O)O`
9C4	4CNP	P24670	208.2 Da LogP -3.35 TPSA 138.5	1 viol.	✓ Clean	`C1[C@H]([C@@H](C([C@@H]([C@]1(C(=O)O)O)O)O)O)O`
9PY	4CNO	P24670	204.2 Da LogP -1.87 TPSA 115.1	✓ Ro5	✓ Clean	`C[C@H]1C(=O)[C@H]([C@@H](C[C@@]1(C(=O)O)O)O)O`
BO3	3S42	P58687	61.8 Da LogP -2.05 TPSA 60.7	✓ Ro5	✓ Clean	`B(O)(O)O`
DHK	1SFJ	Q6GII7	174.2 Da LogP -0.75 TPSA 98.0	✓ Ro5	✓ Clean	`C1[C@@H](C=C([C@H]([C@@H]1O)O)O)C(=O)O`
DHS	3JS3	Q186A6	172.2 Da LogP -2.88 TPSA 106.6	✓ Ro5	✓ Clean	`C1[C@H]([C@@H](C(C=C1C(=O)[O-])N)O)O`
DQA	3M7W	P58687	190.2 Da LogP -2.11 TPSA 115.1	✓ Ro5	✓ Clean	`C1[C@H]([C@@H](C(=O)C[C@]1(C(=O)O)O)O)O`
FQZ	6H5G	P24670	174.2 Da LogP -0.16 TPSA 77.8	✓ Ro5	✓ Clean	`C[C@H]1C[C@H](C[C@H]([C@@H]1O)O)C(=O)O`
FSQ	6H5C	P24670	190.2 Da LogP -1.05 TPSA 98.0	✓ Ro5	✓ Clean	`C[C@]1(C[C@H](C[C@H]([C@@H]1O)O)C(=O)O)O`
FT5	6H5J	P24670	176.2 Da LogP -1.44 TPSA 98.0	✓ Ro5	✓ Clean	`C1[C@H](C(C(CC1C(=O)O)O)O)O`
L9Z	6SFE	P24670	205.2 Da LogP -2.11 TPSA 124.0	✓ Ro5	✓ Clean	`C1[C@@H](C[C@@]([C@H]([C@@H]1O)O)(CN)O)C(=O)O`
MLA	3S42	P58687	104.1 Da LogP -0.45 TPSA 74.6	✓ Ro5	✓ Clean	`C(C(=O)O)C(=O)O`
QIC	4GUI	P58687	192.2 Da LogP -2.32 TPSA 118.2	✓ Ro5	✓ Clean	`C1[C@H](C([C@@H](CC1(C(=O)O)O)O)O)O`
SHL	4H3D	Q186A6	170.1 Da LogP 0.35 TPSA 87.7	✓ Ro5	✓ Clean	`CC1=C(C(=O)C=C(O1)C(=O)O)O`
SIN	4GFS	P58687	118.1 Da LogP -0.06 TPSA 74.6	✓ Ro5	✓ Clean	`C(CC(=O)O)C(=O)O`
SKM	4GUJ	P58687	174.2 Da LogP -1.52 TPSA 98.0	✓ Ro5	✓ Clean	`C1[C@H]([C@@H]([C@@H](C=C1C(=O)O)O)O)O`
VAU	4UIO	P24670	206.2 Da LogP -1.93 TPSA 118.2	✓ Ro5	✓ Clean	`C[C@]1(C[C@](C[C@H]([C@@H]1O)O)(C(=O)O)O)O`
WPL	4CLM	P24670	190.2 Da LogP -1.05 TPSA 98.0	✓ Ro5	✓ Clean	`C[C@H]1C[C@](C[C@H]([C@@H]1O)O)(C(=O)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).

Ligand	UniProt (homolog)	pchembl	MW · LogP · TPSA	Lipinski	PAINS	SMILES
CHEMBL1161028	P05194	—	269.0 Da LogP -1.74 TPSA 115.1	✓ Ro5	✓ Clean	`O=C1C(O)C(O)CC(O)(C(=O)O)C1Br`
CHEMBL1161029	P05194	—	208.1 Da LogP -2.17 TPSA 115.1	✓ Ro5	✓ Clean	`O=C1C(O)C(O)CC(O)(C(=O)O)C1F`
CHEMBL1161030	P05194	—	251.0 Da LogP -0.59 TPSA 94.8	✓ Ro5	Alert	`O=C(O)C1=C(Br)C(=O)[C@@H](O)[C@H](O)C1`

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
ZINC1532902	0.700	206.2 Da LogP -0.86 TPSA 132.1	✓ Ro5	✓ Clean	`O=C(O)CC[C@@](O)(CC(=O)O)C(=O)O`
ZINC2018106	0.700	206.2 Da LogP -0.86 TPSA 132.1	✓ Ro5	✓ Clean	`O=C(O)CC[C@](O)(CC(=O)O)C(=O)O`
ZINC3593496	0.652	206.2 Da LogP -1.16 TPSA 121.1	✓ Ro5	✓ Clean	`COC(=O)C[C@@](O)(CC(=O)O)C(=O)O`
ZINC3593497	0.652	206.2 Da LogP -1.16 TPSA 121.1	✓ Ro5	✓ Clean	`COC(=O)C[C@](O)(CC(=O)O)C(=O)O`
ZINC1587602	0.633	200.1 Da LogP -0.26 TPSA 125.0	✓ Ro5	✓ Clean	`O=C(O)c1cc(=O)c(O)c(C(=O)O)o1`
ZINC14686440	0.625	436.4 Da LogP -2.64 TPSA 247.9	1 viol.	✓ Clean	`O=C(O)C[C@](O)(CC(=O)NCCCCNC(=O)C[C@@](O)(CC(=O…`
ZINC14686442	0.625	436.4 Da LogP -2.64 TPSA 247.9	1 viol.	✓ Clean	`O=C(O)C[C@@](O)(CC(=O)NCCCCNC(=O)C[C@](O)(CC(=O…`
ZINC14686444	0.625	436.4 Da LogP -2.64 TPSA 247.9	1 viol.	✓ Clean	`O=C(O)C[C@@](O)(CC(=O)NCCCCNC(=O)C[C@@](O)(CC(=…`
ZINC400264	0.579	224.3 Da LogP 1.45 TPSA 74.6	✓ Ro5	✓ Clean	`O=C(O)C1CC2C(C1)C1CC(C(=O)O)CC21`
ZINC13398039	0.577	234.2 Da LogP -0.38 TPSA 121.1	✓ Ro5	✓ Clean	`CC(C)OC(=O)C[C@](O)(CC(=O)O)C(=O)O`
ZINC2528012	0.577	234.2 Da LogP -0.38 TPSA 121.1	✓ Ro5	✓ Clean	`CC(C)OC(=O)C[C@@](O)(CC(=O)O)C(=O)O`
ZINC1572706	0.563	260.2 Da LogP -1.05 TPSA 132.8	✓ Ro5	✓ Clean	`O=C(O)CCC(=O)NCCNC(=O)CCC(=O)O`
ZINC146315135	0.560	204.2 Da LogP 0.86 TPSA 94.8	✓ Ro5	✓ Clean	`CCCCC[C@@](O)(CC(=O)O)C(=O)O`
ZINC146315336	0.560	204.2 Da LogP 0.86 TPSA 94.8	✓ Ro5	✓ Clean	`CCCCC[C@](O)(CC(=O)O)C(=O)O`
ZINC1850353	0.556	206.1 Da LogP -0.86 TPSA 132.1	✓ Ro5	✓ Clean	`O=C(O)CC(O)(CC(=O)O)CC(=O)O`
ZINC39233818	0.550	212.2 Da LogP 1.60 TPSA 74.6	✓ Ro5	✓ Clean	`O=C(O)C1CC2CC(C1)CC(C(=O)O)C2`
ZINC85395002	0.548	205.0 Da LogP 2.05 TPSA 50.4	✓ Ro5	✓ Clean	`Cc1oc(C(=O)O)cc1Br`
ZINC35465466	0.529	244.3 Da LogP 2.24 TPSA 91.7	✓ Ro5	✓ Clean	`O=C(O)CCCCCCCC(=O)CCC(=O)O`
ZINC39208104	0.529	262.2 Da LogP -0.20 TPSA 127.2	✓ Ro5	✓ Clean	`O=C(O)CCC(=O)OCCOC(=O)CCC(=O)O`
ZINC13398014	0.522	220.2 Da LogP -1.07 TPSA 110.1	✓ Ro5	✓ Clean	`COC(=O)CC(O)(CC(=O)OC)C(=O)O`
ZINC3861629	0.522	206.1 Da LogP -1.16 TPSA 121.1	✓ Ro5	✓ Clean	`COC(=O)C(O)(CC(=O)O)CC(=O)O`
ZINC4985816	0.514	218.2 Da LogP 2.11 TPSA 67.5	✓ Ro5	✓ Clean	`Cc1cc2oc(C(=O)O)cc(=O)c2cc1C`
ZINC100969993	0.500	359.5 Da LogP 2.70 TPSA 123.9	✓ Ro5	✓ Clean	`CCCCCCCCCCCCNC(=O)C[C@](O)(CC(=O)O)C(=O)O`
ZINC100969996	0.500	359.5 Da LogP 2.70 TPSA 123.9	✓ Ro5	✓ Clean	`CCCCCCCCCCCCNC(=O)C[C@@](O)(CC(=O)O)C(=O)O`
ZINC138079998	0.500	212.0 Da LogP 1.41 TPSA 37.3	✓ Ro5	✓ Clean	`C=C(I)CC(=O)O`
ZINC1542984448	0.500	470.5 Da LogP 0.07 TPSA 148.4	✓ Ro5	✓ Clean	`O=C(O)CCOCCOCCOCCOCCOCCOCCOCCOCCC(=O)O`
ZINC1711854	0.500	248.2 Da LogP -0.13 TPSA 149.2	✓ Ro5	✓ Clean	`O=C(O)CC(CC(=O)O)(CC(=O)O)CC(=O)O`
ZINC22114796	0.500	206.2 Da LogP 0.53 TPSA 104.8	✓ Ro5	✓ Clean	`Cc1oc(C(=O)O)cc1S(=O)(=O)O`
ZINC26897400	0.500	286.4 Da LogP 3.41 TPSA 91.7	✓ Ro5	✓ Clean	`O=C(O)CCCCCCC(=O)CCCCCCC(=O)O`
ZINC3074813	0.500	258.3 Da LogP 2.63 TPSA 91.7	✓ Ro5	✓ Clean	`O=C(O)CCCCCC(=O)CCCCCC(=O)O`
ZINC34423725	0.500	342.5 Da LogP 4.97 TPSA 91.7	✓ Ro5	✓ Clean	`O=C(O)CCCCCCCCC(=O)CCCCCCCCC(=O)O`
ZINC38682833	0.500	286.3 Da LogP -0.61 TPSA 115.2	✓ Ro5	✓ Clean	`O=C(O)CCC(=O)N1CCN(C(=O)CCC(=O)O)CC1`
ZINC4181831	0.500	232.2 Da LogP -0.01 TPSA 129.0	✓ Ro5	✓ Clean	`O=C(O)CCC(=O)C(CC(=O)O)CC(=O)O`
ZINC4822898	0.500	272.3 Da LogP 3.02 TPSA 91.7	✓ Ro5	✓ Clean	`O=C(O)CCCCCCC(=O)CCCCCC(=O)O`
ZINC5536699	0.500	202.2 Da LogP 2.95 TPSA 50.4	✓ Ro5	✓ Clean	`Cc1oc(C(=O)O)cc1-c1ccccc1`
ZINC91366444	0.500	204.2 Da LogP 0.69 TPSA 84.6	✓ Ro5	✓ Clean	`Cc1oc(C(=O)O)cc1S(C)(=O)=O`

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.