Protein profile

KP13_02317

Propanediol dehydratase large subunit

Genome: KpKP13

Gene: pduC AHE42888.1 Structure source: AlphaFold + ColabFold UniProt A0A0H3GXM1

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Amino acids 554

Annotations 3

Features 10

PDB binders 1

Druggability 0.451

Overview

Basic information about this protein and its source genome.

Accession: KP13_02317
Assembly: Klebsiella pneumoniae subsp. pneumoniae Kp13, complete sequence
Gene: pduC AHE42888.1
Status: annotated
Amino acids: 554
Structure source: AlphaFold + ColabFold

GO:0016836 Catalysis of the cleavage of a carbon-oxygen bond by elimination of water. GO:0003824 Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic. GO:0031419 Binding to cobalamin (vitamin B12), a water-soluble vitamin characterized by possession of a corrin nucleus containing a cobalt atom.

Target profile

Computed evidence for target prioritization.

Human off-target: No hit
Human identity (%): 0.0
Gut microbiome off-target: hit
Essential (DEG): N
DEG identity (%): 0.0
Localization: Cytoplasmic
ColabFold pLDDT: 98.48

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 0.451

Structure A0A0H3GXM1

Pocket Pocket 8

P2Rank 0.71

Structure A0A0H3GXM1

Pocket Pocket 1

ColabFold model

FPocket 0.471 · Pocket 4

P2Rank 0.687 · Pocket 1

Core conservation Conserved core gene

Roary core

CoreCruncher core

Gut microbiome 185 / 4744 genomes with a hit

Normalized 0.039

Sequence

Primary amino-acid sequence viewer.

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

3 GO

Gene Ontology (GO)

GO:0016836 Catalysis of the cleavage of a carbon-oxygen bond by elimination of water.
GO:0003824 Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
GO:0031419 Binding to cobalamin (vitamin B12), a water-soluble vitamin characterized by possession of a corrin nucleus containing a cobalt atom.

Sequence Features

Domain/signature hits from InterPro and related databases.

10 records

Show feature table

Start	End	DB	Term	Name
1	551	Pfam	PF02286	Dehydratase large subunit
1	551	InterPro	IPR003206	Diol/glycerol dehydratase, large subunit
1	553	SUPERFAMILY	SSF51703	Cobalamin (vitamin B12)-dependent enzymes
1	553	InterPro	IPR016176	Cobalamin (vitamin B12)-dependent enzyme, catalytic
1	554	PIRSF	PIRSF018507	Prpndl_dhdrts_lg
1	554	InterPro	IPR003206	Diol/glycerol dehydratase, large subunit
1	554	Gene3D	G3DSA:3.20.20.350	Diol/glycerol dehydratase, large subunit
1	554	InterPro	IPR036999	Diol/glycerol dehydratase, large subunit superfamily
8	552	CDD	cd03687	Dehydratase_LU
8	552	InterPro	IPR003206	Diol/glycerol dehydratase, large subunit

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_A0A0H3GXM1	AlphaFold	—	—	full sequence	—	Viewing
ColabFold KP13_02317	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
8				0.451

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	Score	Probability
1	9.75	0.524
2	3.27	0.114
3	2.63	0.077
4	1.67	0.028
5	1.22	0.011

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
4				0.471
9				0.283

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	Score	Probability
1	9.47	0.509
2	4.61	0.199
3	2.84	0.089
4	2.75	0.083

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.

51 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
5AD	5YRT	Q59470	251.2 Da LogP -0.95 TPSA 119.3	✓ Ro5	✓ Clean	`C[C@@H]1[C@H]([C@H]([C@@H](O1)n2cnc3c2ncnc3N)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
ZINC100352250	1.000	251.2 Da LogP -0.95 TPSA 119.3	✓ Ro5	✓ Clean	`C[C@@H]1O[C@H](n2cnc3c(N)ncnc32)[C@H](O)[C@@H]1O`
ZINC1095430	1.000	251.2 Da LogP -0.95 TPSA 119.3	✓ Ro5	✓ Clean	`C[C@H]1O[C@@H](n2cnc3c(N)ncnc32)[C@H](O)[C@H]1O`
ZINC13542750	1.000	251.2 Da LogP -0.95 TPSA 119.3	✓ Ro5	✓ Clean	`C[C@@H]1O[C@H](n2cnc3c(N)ncnc32)[C@@H](O)[C@@H]…`
ZINC135734	1.000	251.2 Da LogP -0.95 TPSA 119.3	✓ Ro5	✓ Clean	`C[C@@H]1O[C@H](n2cnc3c(N)ncnc32)[C@@H](O)[C@H]1O`
ZINC17005625	1.000	251.2 Da LogP -0.95 TPSA 119.3	✓ Ro5	✓ Clean	`C[C@@H]1O[C@H](n2cnc3c(N)ncnc32)[C@H](O)[C@H]1O`
ZINC1999286	1.000	251.2 Da LogP -0.95 TPSA 119.3	✓ Ro5	✓ Clean	`C[C@H]1O[C@@H](n2cnc3c(N)ncnc32)[C@H](O)[C@@H]1O`
ZINC3869309	1.000	251.2 Da LogP -0.95 TPSA 119.3	✓ Ro5	✓ Clean	`C[C@H]1O[C@@H](n2cnc3c(N)ncnc32)[C@@H](O)[C@H]1O`
ZINC3869310	1.000	251.2 Da LogP -0.95 TPSA 119.3	✓ Ro5	✓ Clean	`C[C@@H]1O[C@@H](n2cnc3c(N)ncnc32)[C@@H](O)[C@H]…`
ZINC3869311	1.000	251.2 Da LogP -0.95 TPSA 119.3	✓ Ro5	✓ Clean	`C[C@H]1O[C@@H](n2cnc3c(N)ncnc32)[C@@H](O)[C@@H]…`
ZINC3869312	1.000	251.2 Da LogP -0.95 TPSA 119.3	✓ Ro5	✓ Clean	`C[C@@H]1O[C@@H](n2cnc3c(N)ncnc32)[C@@H](O)[C@@H…`
ZINC1702626	0.974	281.3 Da LogP -1.59 TPSA 139.5	✓ Ro5	✓ Clean	`C[C@H]1O[C@@H](n2cnc3c(N)ncnc32)[C@@H](O)[C@@H]…`
ZINC4821676	0.974	281.3 Da LogP -1.59 TPSA 139.5	✓ Ro5	✓ Clean	`C[C@@H]1O[C@@H](n2cnc3c(N)ncnc32)[C@@H](O)[C@@H…`
ZINC4821679	0.974	281.3 Da LogP -1.59 TPSA 139.5	✓ Ro5	✓ Clean	`C[C@H]1O[C@@H](n2cnc3c(N)ncnc32)[C@@H](O)[C@@H]…`
ZINC4821682	0.974	281.3 Da LogP -1.59 TPSA 139.5	✓ Ro5	✓ Clean	`C[C@@H]1O[C@@H](n2cnc3c(N)ncnc32)[C@@H](O)[C@@H…`
ZINC5139067	0.721	283.3 Da LogP -1.04 TPSA 119.3	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@H](CS)[C@@H](O)[C@H]1O`
ZINC2047403	0.705	267.2 Da LogP -1.98 TPSA 139.5	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@H]1O[C@@H](CO)[C@@H](O)[C@@H]1O`
ZINC2047673	0.705	267.2 Da LogP -1.98 TPSA 139.5	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@@H](CO)[C@H](O)[C@@H]1O`
ZINC2169830	0.705	267.2 Da LogP -1.98 TPSA 139.5	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@H](CO)[C@@H](O)[C@H]1O`
ZINC3201876	0.705	267.2 Da LogP -1.98 TPSA 139.5	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@H]1O[C@H](CO)[C@@H](O)[C@@H]1O`
ZINC3201878	0.705	267.2 Da LogP -1.98 TPSA 139.5	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@@H](CO)[C@@H](O)[C@@H]…`
ZINC3814316	0.705	266.3 Da LogP -2.01 TPSA 145.3	✓ Ro5	✓ Clean	`NC[C@H]1O[C@@H](n2cnc3c(N)ncnc32)[C@H](O)[C@@H]…`
ZINC3830178	0.705	267.2 Da LogP -1.98 TPSA 139.5	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@H]1O[C@@H](CO)[C@@H](O)[C@H]1O`
ZINC3830179	0.705	267.2 Da LogP -1.98 TPSA 139.5	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@@H](CO)[C@@H](O)[C@H]1O`
ZINC3978047	0.705	267.2 Da LogP -1.98 TPSA 139.5	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@@H](CO)[C@H](O)[C@H]1O`
ZINC3978048	0.705	267.2 Da LogP -1.98 TPSA 139.5	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@H]1O[C@H](CO)[C@H](O)[C@H]1O`
ZINC3978049	0.705	267.2 Da LogP -1.98 TPSA 139.5	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@H](CO)[C@H](O)[C@H]1O`
ZINC4048240	0.705	267.2 Da LogP -1.98 TPSA 139.5	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@H]1O[C@H](CO)[C@@H](O)[C@H]1O`
ZINC4773848	0.705	266.3 Da LogP -2.01 TPSA 145.3	✓ Ro5	✓ Clean	`NC[C@@H]1O[C@H](n2cnc3c(N)ncnc32)[C@H](O)[C@@H]…`
ZINC4773849	0.705	266.3 Da LogP -2.01 TPSA 145.3	✓ Ro5	✓ Clean	`NC[C@@H]1O[C@@H](n2cnc3c(N)ncnc32)[C@H](O)[C@@H…`
ZINC4773850	0.705	266.3 Da LogP -2.01 TPSA 145.3	✓ Ro5	✓ Clean	`NC[C@@H]1O[C@H](n2cnc3c(N)ncnc32)[C@@H](O)[C@@H…`
ZINC4773851	0.705	266.3 Da LogP -2.01 TPSA 145.3	✓ Ro5	✓ Clean	`NC[C@@H]1O[C@@H](n2cnc3c(N)ncnc32)[C@@H](O)[C@@…`
ZINC77981211	0.705	266.3 Da LogP -2.01 TPSA 145.3	✓ Ro5	✓ Clean	`NC[C@H]1O[C@@H](n2cnc3c(N)ncnc32)[C@@H](O)[C@H]…`
ZINC82228511	0.705	266.3 Da LogP -2.01 TPSA 145.3	✓ Ro5	✓ Clean	`NC[C@H]1O[C@@H](n2cnc3c(N)ncnc32)[C@H](O)[C@H]1O`
ZINC8580514	0.705	267.2 Da LogP -1.98 TPSA 139.5	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@H](CO)[C@H](O)[C@@H]1O`
ZINC895113	0.705	267.2 Da LogP -1.98 TPSA 139.5	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@H]1O[C@@H](CO)[C@H](O)[C@@H]1O`
ZINC896706	0.705	267.2 Da LogP -1.98 TPSA 139.5	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@H]1O[C@@H](CO)[C@H](O)[C@H]1O`
ZINC970363	0.705	267.2 Da LogP -1.98 TPSA 139.5	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@H](CO)[C@@H](O)[C@@H]1O`
ZINC1081541	0.689	285.7 Da LogP -0.73 TPSA 119.3	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@H](CCl)[C@@H](O)[C@@H]…`
ZINC4188096	0.689	297.3 Da LogP -2.62 TPSA 159.8	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@H]1O[C@@H](CO)[C@@H](O)[C@@H](…`
ZINC4188103	0.689	297.3 Da LogP -2.62 TPSA 159.8	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@@H](CO)[C@@H](O)[C@@H]…`
ZINC4188112	0.689	297.3 Da LogP -2.62 TPSA 159.8	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@H]1O[C@@H](CO)[C@@H](O)[C@@H](…`
ZINC4188116	0.689	297.3 Da LogP -2.62 TPSA 159.8	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@@H](CO)[C@@H](O)[C@@H]…`
ZINC5941240	0.689	269.2 Da LogP -1.00 TPSA 119.3	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@H](CF)[C@@H](O)[C@H]1O`
ZINC100349915	0.681	297.3 Da LogP -0.61 TPSA 119.3	✓ Ro5	✓ Clean	`CSC[C@@H]1O[C@H](n2cnc3c(N)ncnc32)[C@H](O)[C@@H…`
ZINC105279440	0.681	297.3 Da LogP -0.61 TPSA 119.3	✓ Ro5	✓ Clean	`CSC[C@H]1O[C@H](n2cnc3c(N)ncnc32)[C@H](O)[C@H]1O`
ZINC25963247	0.681	297.3 Da LogP -0.61 TPSA 119.3	✓ Ro5	✓ Clean	`CSC[C@H]1O[C@H](n2cnc3c(N)ncnc32)[C@@H](O)[C@H]…`
ZINC3869319	0.681	297.3 Da LogP -0.61 TPSA 119.3	✓ Ro5	✓ Clean	`CSC[C@H]1O[C@@H](n2cnc3c(N)ncnc32)[C@@H](O)[C@H…`
ZINC4228245	0.681	297.3 Da LogP -0.61 TPSA 119.3	✓ Ro5	✓ Clean	`CSC[C@H]1O[C@@H](n2cnc3c(N)ncnc32)[C@H](O)[C@@H…`
ZINC5929300	0.681	297.3 Da LogP -0.61 TPSA 119.3	✓ Ro5	✓ Clean	`CSC[C@H]1O[C@@H](n2cnc3c(N)ncnc32)[C@H](O)[C@H]…`
ZINC895091	0.681	297.3 Da LogP -0.61 TPSA 119.3	✓ Ro5	✓ Clean	`CSC[C@@H]1O[C@H](n2cnc3c(N)ncnc32)[C@@H](O)[C@H…`

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.