Protein profile

KP13_31530

dTDP-D-glucose 4,6-dehydratase in cps region

Genome: KpKP13

Gene: AHE43664.1 rmlB Structure source: AlphaFold + ColabFold UniProt A0A0H3GVT8

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Amino acids 354

Annotations 3

Features 22

PDB binders 3

Druggability 0.991

Overview

Basic information about this protein and its source genome.

Accession: KP13_31530
Assembly: Klebsiella pneumoniae subsp. pneumoniae Kp13, complete sequence
Gene: AHE43664.1 rmlB
Status: annotated
Amino acids: 354
Structure source: AlphaFold + ColabFold

4.2.1.46

GO:0008460 Catalysis of the reaction: dTDP-glucose = dTDP-4-dehydro-6-deoxy-alpha-D-glucose + H2O. GO:0009225 The cellular chemical reactions and pathways involving nucleotide-sugars, any nucleotide-carbohydrate in which the distal phosphoric residue of a nucleoside 5'-diphosphate is in glycosidic linkage with a monosaccharide or monosaccharide derivative.

Target profile

Computed evidence for target prioritization.

Human off-target: hit
Human identity (%): 35.0
Human E-value: 1.03e-65
Gut microbiome off-target: hit
Essential (DEG): Y
DEG identity (%): 70.536
DEG E-value: 0.0
Localization: Cytoplasmic
ColabFold pLDDT: 95.05

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 0.991

Structure A0A0H3GVT8

Pocket Pocket 1

P2Rank 0.99

Structure A0A0H3GVT8

Pocket Pocket 1

ColabFold model

FPocket 0.833 · Pocket 1

P2Rank 0.992 · Pocket 1

Core conservation Accessory gene

Roary accessory

CoreCruncher accessory

Gut microbiome 1656 / 4744 genomes with a hit

Normalized 0.349

Sequence

Primary amino-acid sequence viewer.

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 2 GO

Enzyme Commission (EC)

4.2.1.46

Gene Ontology (GO)

GO:0008460 Catalysis of the reaction: dTDP-glucose = dTDP-4-dehydro-6-deoxy-alpha-D-glucose + H2O.
GO:0009225 The cellular chemical reactions and pathways involving nucleotide-sugars, any nucleotide-carbohydrate in which the distal phosphoric residue of a nucleoside 5'-diphosphate is in glycosidic linkage with a monosaccharide or monosaccharide derivative.

Sequence Features

Domain/signature hits from InterPro and related databases.

22 records

Show feature table

Start	End	DB	Term	Name
1	2	Phobius	SIGNAL_PEPTIDE_N_REGION	N-terminal region of a signal peptide.
2	339	NCBIfam	TIGR01181	dTDP-glucose 4,6-dehydratase
2	339	InterPro	IPR005888	dTDP-glucose 4,6-dehydratase
1	18	Phobius	SIGNAL_PEPTIDE	Signal peptide region
200	334	Gene3D	G3DSA:3.90.25.10	-
19	354	Phobius	NON_CYTOPLASMIC_DOMAIN	Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
2	324	Gene3D	G3DSA:3.40.50.720	-
4	326	Pfam	PF16363	GDP-mannose 4,6 dehydratase
4	326	InterPro	IPR016040	NAD(P)-binding domain
1	334	CDD	cd05246	dTDP_GD_SDR_e
1	334	InterPro	IPR005888	dTDP-glucose 4,6-dehydratase
1	344	SUPERFAMILY	SSF51735	NAD(P)-binding Rossmann-fold domains
1	344	InterPro	IPR036291	NAD(P)-binding domain superfamily
14	18	Phobius	SIGNAL_PEPTIDE_C_REGION	C-terminal region of a signal peptide.
2	341	PANTHER	PTHR43000	DTDP-D-GLUCOSE 4,6-DEHYDRATASE-RELATED
2	19	PRINTS	PR00081	Glucose/ribitol dehydrogenase family signature
2	19	InterPro	IPR002347	Short-chain dehydrogenase/reductase SDR
159	178	PRINTS	PR00081	Glucose/ribitol dehydrogenase family signature
159	178	InterPro	IPR002347	Short-chain dehydrogenase/reductase SDR
38	49	PRINTS	PR00081	Glucose/ribitol dehydrogenase family signature
38	49	InterPro	IPR002347	Short-chain dehydrogenase/reductase SDR
3	13	Phobius	SIGNAL_PEPTIDE_H_REGION	Hydrophobic region of a signal peptide.

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_A0A0H3GVT8	AlphaFold	—	—	full sequence	—	Viewing
ColabFold KP13_31530	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
1				0.991
5				0.503
3				0.218

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				45.59	0.973

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				0.833

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				54.32	0.984

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.

53 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
DAU	1KEU	P26391	564.3 Da LogP -3.46 TPSA 276.8	3 viol.	✓ Clean	`CC1=CN(C(=O)NC1=O)[C@H]2C[C@@H]([C@H](O2)CO[P@]…`
TDX	1KEP	Q8GIP9	534.3 Da LogP -2.82 TPSA 256.5	3 viol.	✓ Clean	`CC1=CN(C(=O)NC1=O)[C@H]2C[C@@H]([C@H](O2)CO[P@]…`
TYD	1KEW	P26391	402.2 Da LogP -1.28 TPSA 197.6	✓ Ro5	✓ Clean	`CC1=CN(C(=O)NC1=O)[C@H]2C[C@@H]([C@H](O2)CO[P@]…`

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
ZINC33979243	1.000	402.2 Da LogP -1.28 TPSA 197.6	✓ Ro5	✓ Clean	`Cc1cn([C@@H]2C[C@H](O)[C@H](CO[P@@](=O)(O)OP(=O…`
ZINC13507072	0.754	482.2 Da LogP -1.16 TPSA 244.1	2 viol.	✓ Clean	`Cc1cn([C@@H]2C[C@@H](O)[C@H](CO[P@@](=O)(O)O[P@…`
ZINC33979251	0.754	482.2 Da LogP -1.16 TPSA 244.1	2 viol.	✓ Clean	`Cc1cn([C@@H]2C[C@H](O)[C@H](CO[P@@](=O)(O)O[P@@…`
ZINC12503053	0.750	402.2 Da LogP -1.28 TPSA 197.6	✓ Ro5	✓ Clean	`Cc1cn([C@@H]2C[C@H](O)[C@@H](CO[P@@](=O)(O)OP(=…`
ZINC33979244	0.750	402.2 Da LogP -1.28 TPSA 197.6	✓ Ro5	✓ Clean	`Cc1cn([C@H]2C[C@H](O)[C@H](CO[P@@](=O)(O)OP(=O)…`
ZINC33979245	0.750	402.2 Da LogP -1.28 TPSA 197.6	✓ Ro5	✓ Clean	`Cc1cn([C@@H]2C[C@@H](O)[C@H](CO[P@@](=O)(O)OP(=…`
ZINC33979246	0.750	402.2 Da LogP -1.28 TPSA 197.6	✓ Ro5	✓ Clean	`Cc1cn([C@H]2C[C@@H](O)[C@H](CO[P@@](=O)(O)OP(=O…`
ZINC8215882	0.750	402.2 Da LogP -1.28 TPSA 197.6	✓ Ro5	✓ Clean	`Cc1cn([C@H]2C[C@H](O)[C@@H](CO[P@@](=O)(O)OP(=O…`
ZINC13523519	0.683	322.2 Da LogP -1.40 TPSA 151.1	✓ Ro5	✓ Clean	`Cc1cn([C@@H]2C[C@@H](O)[C@@H](COP(=O)(O)O)O2)c(…`
ZINC1532628	0.683	322.2 Da LogP -1.40 TPSA 151.1	✓ Ro5	✓ Clean	`Cc1cn([C@@H]2C[C@@H](O)[C@H](COP(=O)(O)O)O2)c(=…`
ZINC1678872	0.683	322.2 Da LogP -1.40 TPSA 151.1	✓ Ro5	✓ Clean	`Cc1cn([C@H]2C[C@H](O)[C@@H](COP(=O)(O)O)O2)c(=O…`
ZINC2047010	0.683	322.2 Da LogP -1.40 TPSA 151.1	✓ Ro5	✓ Clean	`Cc1cn([C@H]2C[C@@H](O)[C@H](COP(=O)(O)O)O2)c(=O…`
ZINC3870253	0.683	322.2 Da LogP -1.40 TPSA 151.1	✓ Ro5	✓ Clean	`Cc1cn([C@@H]2C[C@H](O)[C@H](COP(=O)(O)O)O2)c(=O…`
ZINC3870254	0.683	322.2 Da LogP -1.40 TPSA 151.1	✓ Ro5	✓ Clean	`Cc1cn([C@H]2C[C@H](O)[C@H](COP(=O)(O)O)O2)c(=O)…`
ZINC6523446	0.683	322.2 Da LogP -1.40 TPSA 151.1	✓ Ro5	✓ Clean	`Cc1cn([C@@H]2C[C@H](O)[C@@H](COP(=O)(O)O)O2)c(=…`
ZINC138164075	0.647	498.2 Da LogP 0.21 TPSA 227.1	2 viol.	✓ Clean	`Cc1cn([C@@H]2C[C@H](O)[C@H](CO[P@@](=O)(O)O[P@@…`
ZINC111459735	0.642	481.2 Da LogP -1.20 TPSA 249.9	2 viol.	✓ Clean	`Cc1cn([C@@H]2C[C@H](N)[C@H](CO[P@@](=O)(O)O[P@@…`
ZINC17107637	0.635	320.2 Da LogP -1.46 TPSA 162.7	✓ Ro5	✓ Clean	`Cc1cn([C@@H]2C[C@@H](O)[C@@H](COP(N)(N)=O)O2)c(…`
ZINC17107641	0.635	320.2 Da LogP -1.46 TPSA 162.7	✓ Ro5	✓ Clean	`Cc1cn([C@@H]2C[C@H](O)[C@@H](COP(N)(N)=O)O2)c(=…`
ZINC5493427	0.635	320.2 Da LogP -1.46 TPSA 162.7	✓ Ro5	✓ Clean	`Cc1cn([C@@H]2C[C@H](O)[C@H](COP(N)(N)=O)O2)c(=O…`
ZINC5493430	0.635	320.2 Da LogP -1.46 TPSA 162.7	✓ Ro5	✓ Clean	`Cc1cn([C@@H]2C[C@@H](O)[C@H](COP(N)(N)=O)O2)c(=…`
ZINC13520531	0.634	443.3 Da LogP 0.60 TPSA 183.2	✓ Ro5	✓ Clean	`Cc1cn([C@H]2C[C@H](O)[C@@H](CO[P@](=O)(O)Oc3ccc…`
ZINC142512519	0.627	498.2 Da LogP 0.21 TPSA 227.1	2 viol.	✓ Clean	`Cc1cn([C@@H]2C[C@H](O)[C@H](CO[P@@](=O)(O)O[P@@…`
ZINC113218151	0.612	486.1 Da LogP -1.33 TPSA 244.1	2 viol.	✓ Clean	`O=c1[nH]c(=O)n([C@H]2C[C@H](O)[C@@H](CO[P@](=O)…`
ZINC80168152	0.612	486.1 Da LogP -1.33 TPSA 244.1	2 viol.	✓ Clean	`O=c1[nH]c(=O)n([C@@H]2C[C@H](O)[C@H](CO[P@@](=O…`
ZINC59206718	0.609	498.2 Da LogP -1.98 TPSA 264.4	2 viol.	✓ Clean	`O=c1[nH]c(=O)n([C@@H]2C[C@H](O)[C@H](CO[P@@](=O…`
ZINC13519607	0.603	498.2 Da LogP -2.19 TPSA 264.4	2 viol.	✓ Clean	`Cc1cn([C@@H]2O[C@H](CO[P@](=O)(O)O[P@](=O)(O)OP…`
ZINC31298140	0.603	498.2 Da LogP -2.19 TPSA 264.4	2 viol.	✓ Clean	`Cc1cn([C@@H]2O[C@H](CO[P@@](=O)(O)O[P@@](=O)(O)…`
ZINC81168754	0.603	498.2 Da LogP -2.19 TPSA 264.4	2 viol.	✓ Clean	`Cc1cn([C@@H]2O[C@H](CO[P@@](=O)(O)O[P@@](=O)(O)…`
ZINC81168756	0.603	498.2 Da LogP -2.19 TPSA 264.4	2 viol.	✓ Clean	`Cc1cn([C@@H]2O[C@H](CO[P@@](=O)(O)O[P@@](=O)(O)…`
ZINC6521315	0.600	322.2 Da LogP -1.40 TPSA 151.1	✓ Ro5	✓ Clean	`Cc1cn([C@H]2C[C@H](OP(=O)(O)O)[C@@H](CO)O2)c(=O…`
ZINC13518650	0.597	418.2 Da LogP -2.31 TPSA 217.8	1 viol.	✓ Clean	`Cc1cn([C@@H]2O[C@H](CO[P@@](=O)(O)OP(=O)(O)O)[C…`
ZINC4804742	0.597	272.3 Da LogP -2.15 TPSA 124.8	✓ Ro5	✓ Clean	`Cc1cn([C@@H]2C[C@H](O)[C@H](O)[C@H](CO)O2)c(=O)…`
ZINC4804743	0.597	272.3 Da LogP -2.15 TPSA 124.8	✓ Ro5	✓ Clean	`Cc1cn([C@H]2C[C@H](O)[C@H](O)[C@H](CO)O2)c(=O)[…`
ZINC4804744	0.597	272.3 Da LogP -2.15 TPSA 124.8	✓ Ro5	✓ Clean	`Cc1cn([C@@H]2C[C@@H](O)[C@H](O)[C@H](CO)O2)c(=O…`
ZINC4804745	0.597	272.3 Da LogP -2.15 TPSA 124.8	✓ Ro5	✓ Clean	`Cc1cn([C@H]2C[C@@H](O)[C@H](O)[C@H](CO)O2)c(=O)…`
ZINC138954515	0.594	496.2 Da LogP -1.66 TPSA 261.2	2 viol.	✓ Clean	`O=Cc1cn([C@@H]2C[C@H](O)[C@H](CO[P@@](=O)(O)O[P…`
ZINC11422512	0.591	402.2 Da LogP -1.28 TPSA 197.6	✓ Ro5	✓ Clean	`Cc1cn([C@H]2C[C@H](OP(=O)(O)O)[C@@H](COP(=O)(O)…`
ZINC1842580	0.590	242.2 Da LogP -1.51 TPSA 104.5	✓ Ro5	✓ Clean	`Cc1cn([C@@H]2C[C@H](O)[C@H](CO)O2)c(=O)[nH]c1=O`
ZINC2159	0.590	242.2 Da LogP -1.51 TPSA 104.5	✓ Ro5	✓ Clean	`Cc1cn([C@@H]2C[C@@H](O)[C@H](CO)O2)c(=O)[nH]c1=O`
ZINC2545102	0.590	242.2 Da LogP -1.51 TPSA 104.5	✓ Ro5	✓ Clean	`Cc1cn([C@H]2C[C@@H](O)[C@H](CO)O2)c(=O)[nH]c1=O`
ZINC25672	0.590	242.2 Da LogP -1.51 TPSA 104.5	✓ Ro5	✓ Clean	`Cc1cn([C@H]2C[C@H](O)[C@@H](CO)O2)c(=O)[nH]c1=O`
ZINC2572653	0.590	242.2 Da LogP -1.51 TPSA 104.5	✓ Ro5	✓ Clean	`Cc1cn([C@@H]2C[C@@H](O)[C@@H](CO)O2)c(=O)[nH]c1…`
ZINC3831529	0.590	242.2 Da LogP -1.51 TPSA 104.5	✓ Ro5	✓ Clean	`Cc1cn([C@H]2C[C@H](O)[C@H](CO)O2)c(=O)[nH]c1=O`
ZINC5765078	0.590	242.2 Da LogP -1.51 TPSA 104.5	✓ Ro5	✓ Clean	`Cc1cn([C@H]2C[C@@H](O)[C@@H](CO)O2)c(=O)[nH]c1=O`
ZINC6072455	0.590	242.2 Da LogP -1.51 TPSA 104.5	✓ Ro5	✓ Clean	`Cc1cn([C@@H]2C[C@H](O)[C@@H](CO)O2)c(=O)[nH]c1=O`
ZINC6667024	0.581	256.3 Da LogP -0.86 TPSA 93.5	✓ Ro5	✓ Clean	`COC[C@H]1O[C@@H](n2cc(C)c(=O)[nH]c2=O)C[C@@H]1O`
ZINC13519271	0.574	466.2 Da LogP -0.13 TPSA 223.9	✓ Ro5	✓ Clean	`Cc1cn([C@H]2CC[C@@H](CO[P@@](=O)(O)O[P@@](=O)(O…`
ZINC13546289	0.574	466.2 Da LogP -0.13 TPSA 223.9	✓ Ro5	✓ Clean	`Cc1cn([C@@H]2CC[C@H](CO[P@@](=O)(O)O[P@@](=O)(O…`
ZINC6090961	0.569	387.1 Da LogP -0.94 TPSA 151.1	✓ Ro5	✓ Clean	`O=c1[nH]c(=O)n([C@H]2C[C@H](O)[C@@H](COP(=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.