Protein profile

KP13_00591

Rhamnulokinase

Genome: KpKP13

Gene: AHE47066.1 rhaB Structure source: AlphaFold + ColabFold UniProt A0A0H3GGX5

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Amino acids 488

Annotations 9

Features 19

PDB binders 3

Druggability 0.316

Overview

Basic information about this protein and its source genome.

Accession: KP13_00591
Assembly: Klebsiella pneumoniae subsp. pneumoniae Kp13, complete sequence
Gene: AHE47066.1 rhaB
Status: annotated
Amino acids: 488
Structure source: AlphaFold + ColabFold

2.7.1.5

GO:0019301 The chemical reactions and pathways resulting in the breakdown of rhamnose, the hexose 6-deoxy-L-mannose. GO:0005975 The chemical reactions and pathways involving carbohydrates, any of a group of organic compounds based of the general formula Cx(H2O)y. GO:0016301 Catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule. GO:0008993 Catalysis of the reaction: ATP + L-rhamnulose = ADP + L-rhamnulose 1-phosphate. GO:0005829 The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes. GO:0005524 Binding to ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.

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: 95.58

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 0.316

Structure A0A0H3GGX5

Pocket Pocket 23

P2Rank 0.976

Structure A0A0H3GGX5

Pocket Pocket 1

ColabFold model

FPocket 0.801 · Pocket 1

P2Rank 0.971 · Pocket 1

Core conservation Conserved core gene

Roary core

CoreCruncher core

Gut microbiome 76 / 4744 genomes with a hit

Normalized 0.016

Sequence

Primary amino-acid sequence viewer.

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 8 GO

Enzyme Commission (EC)

2.7.1.5

Gene Ontology (GO)

GO:0019301 The chemical reactions and pathways resulting in the breakdown of rhamnose, the hexose 6-deoxy-L-mannose.
GO:0005975 The chemical reactions and pathways involving carbohydrates, any of a group of organic compounds based of the general formula Cx(H2O)y.
GO:0016301 Catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule.
GO:0008993 Catalysis of the reaction: ATP + L-rhamnulose = ADP + L-rhamnulose 1-phosphate.
GO:0005829 The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
GO:0005524 Binding to ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
GO:0004370 Catalysis of the reaction: ATP + glycerol = sn-glycerol 3-phosphate + ADP + 2 H+.
GO:0006071 The chemical reactions and pathways involving glycerol, 1,2,3-propanetriol, a sweet, hygroscopic, viscous liquid, widely distributed in nature as a constituent of many lipids.

Sequence Features

Domain/signature hits from InterPro and related databases.

19 records

Show feature table

Start	End	DB	Term	Name
6	245	SUPERFAMILY	SSF53067	Actin-like ATPase domain
6	245	InterPro	IPR043129	ATPase, nucleotide binding domain
251	471	SUPERFAMILY	SSF53067	Actin-like ATPase domain
251	471	InterPro	IPR043129	ATPase, nucleotide binding domain
3	236	FunFam	G3DSA:3.30.420.40:FF:000064	Rhamnulokinase
237	488	FunFam	G3DSA:3.30.420.40:FF:000073	Rhamnulokinase
6	483	Hamap	MF_01535	Rhamnulokinase [rhaB].
6	483	InterPro	IPR013449	Rhamnulokinase
7	242	Pfam	PF00370	FGGY family of carbohydrate kinases, N-terminal domain
7	242	InterPro	IPR018484	Carbohydrate kinase, FGGY, N-terminal
5	437	CDD	cd07771	FGGY_RhuK
5	437	InterPro	IPR013449	Rhamnulokinase
1	236	Gene3D	G3DSA:3.30.420.40	-
253	439	Pfam	PF02782	FGGY family of carbohydrate kinases, C-terminal domain
253	439	InterPro	IPR018485	Carbohydrate kinase, FGGY, C-terminal
7	470	PANTHER	PTHR10196	SUGAR KINASE
7	459	NCBIfam	TIGR02627	rhamnulokinase
7	459	InterPro	IPR013449	Rhamnulokinase
237	488	Gene3D	G3DSA:3.30.420.40	-

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_A0A0H3GGX5	AlphaFold	—	—	full sequence	—	Viewing
ColabFold KP13_00591	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
23				0.316

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	33.62	0.947
2	2.71	0.081
3	1.99	0.042
4	1.39	0.017
5	1.19	0.01

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				0.801

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	33.78	0.947
2	1.26	0.013
3	1.2	0.011
4	0.58	0.0
5	0.5	0.0

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
DXP	3LL3	Q5FM28	214.1 Da LogP -1.59 TPSA 124.3	✓ Ro5	✓ Clean	`CC(=O)[C@H]([C@@H](COP(=O)(O)O)O)O`
LFR	2CGL	P32171	180.2 Da LogP -3.22 TPSA 110.4	✓ Ro5	✓ Clean	`C([C@H]1[C@@H]([C@H]([C@@](O1)(CO)O)O)O)O`
XUL	3LL3	Q5FM28	150.1 Da LogP -2.74 TPSA 98.0	✓ Ro5	✓ Clean	`C([C@H]([C@@H](C(=O)CO)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).

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
ZINC13551953	0.875	210.2 Da LogP -3.86 TPSA 130.6	1 viol.	✓ Clean	`OC[C@H]1O[C@](O)(CO)[C@@H](O)[C@@H](O)[C@@H]1O`
ZINC13761953	0.875	210.2 Da LogP -3.86 TPSA 130.6	1 viol.	✓ Clean	`OC[C@H]1O[C@@](O)(CO)[C@H](O)[C@@H](O)[C@@H]1O`
ZINC4095790	0.875	210.2 Da LogP -3.86 TPSA 130.6	1 viol.	✓ Clean	`OC[C@H]1O[C@](O)(CO)[C@@H](O)[C@H](O)[C@@H]1O`
ZINC4097479	0.875	210.2 Da LogP -3.86 TPSA 130.6	1 viol.	✓ Clean	`OC[C@H]1O[C@@](O)(CO)[C@@H](O)[C@@H](O)[C@@H]1O`
ZINC65743154	0.875	210.2 Da LogP -3.86 TPSA 130.6	1 viol.	✓ Clean	`OC[C@@H]1O[C@](O)(CO)[C@@H](O)[C@H](O)[C@@H]1O`
ZINC65743155	0.875	210.2 Da LogP -3.86 TPSA 130.6	1 viol.	✓ Clean	`OC[C@H]1O[C@](O)(CO)[C@H](O)[C@H](O)[C@@H]1O`
ZINC65743156	0.875	210.2 Da LogP -3.86 TPSA 130.6	1 viol.	✓ Clean	`OC[C@@H]1O[C@](O)(CO)[C@H](O)[C@H](O)[C@@H]1O`
ZINC95884212	0.875	210.2 Da LogP -3.86 TPSA 130.6	1 viol.	✓ Clean	`OC[C@H]1O[C@](O)(CO)[C@H](O)[C@@H](O)[C@@H]1O`
ZINC100036265	0.682	210.2 Da LogP -4.02 TPSA 138.5	1 viol.	✓ Clean	`O=C(CO)[C@@H](O)[C@@H](O)[C@H](O)[C@H](O)CO`
ZINC100071552	0.682	210.2 Da LogP -4.02 TPSA 138.5	1 viol.	✓ Clean	`O=C(CO)[C@@H](O)[C@@H](O)[C@@H](O)[C@@H](O)CO`
ZINC113074329	0.682	210.2 Da LogP -4.02 TPSA 138.5	1 viol.	✓ Clean	`O=C(CO)[C@H](O)[C@@H](O)[C@H](O)[C@H](O)CO`
ZINC13522679	0.682	210.2 Da LogP -4.02 TPSA 138.5	1 viol.	✓ Clean	`O=C(CO)[C@@H](O)[C@@H](O)[C@H](O)[C@@H](O)CO`
ZINC4353160	0.682	210.2 Da LogP -4.02 TPSA 138.5	1 viol.	✓ Clean	`O=C(CO)[C@@H](O)[C@@H](O)[C@@H](O)[C@H](O)CO`
ZINC8579422	0.682	210.2 Da LogP -4.02 TPSA 138.5	1 viol.	✓ Clean	`O=C(CO)[C@@H](O)[C@H](O)[C@H](O)[C@H](O)CO`
ZINC34543671	0.645	205.2 Da LogP -1.90 TPSA 138.9	✓ Ro5	Alert	`[N-]=[N+]=NC[C@H]1O[C@](O)(CO)[C@@H](O)[C@@H]1O`
ZINC95921630	0.645	205.2 Da LogP -1.90 TPSA 138.9	✓ Ro5	Alert	`[N-]=[N+]=NC[C@H]1O[C@@](O)(CO)[C@@H](O)[C@@H]1O`
ZINC1529626	0.633	230.1 Da LogP -2.62 TPSA 144.5	✓ Ro5	✓ Clean	`O=C(CO)[C@H](O)[C@@H](O)COP(=O)(O)O`
ZINC1532567	0.633	230.1 Da LogP -2.62 TPSA 144.5	✓ Ro5	✓ Clean	`O=C(CO)[C@H](O)[C@H](O)COP(=O)(O)O`
ZINC1532851	0.633	230.1 Da LogP -2.62 TPSA 144.5	✓ Ro5	✓ Clean	`O=C(CO)[C@@H](O)[C@@H](O)COP(=O)(O)O`
ZINC30320708	0.633	230.1 Da LogP -2.62 TPSA 144.5	✓ Ro5	✓ Clean	`O=C(CO)[C@@H](O)[C@H](O)COP(=O)(O)O`
ZINC3870277	0.633	310.1 Da LogP -2.50 TPSA 191.0	1 viol.	✓ Clean	`O=C(COP(=O)(O)O)[C@H](O)[C@H](O)COP(=O)(O)O`
ZINC5830339	0.613	231.1 Da LogP -2.68 TPSA 156.5	1 viol.	✓ Clean	`O=C(NO)[C@H](O)[C@H](O)COP(=O)(O)O`
ZINC2037887790	0.583	342.3 Da LogP -5.40 TPSA 189.5	2 viol.	✓ Clean	`OC[C@H]1O[C@H](OC[C@@H]2O[C@](O)(CO)[C@H](O)[C@…`
ZINC2037887791	0.583	342.3 Da LogP -5.40 TPSA 189.5	2 viol.	✓ Clean	`OC[C@H]1O[C@H](OC[C@@H]2O[C@](O)(CO)[C@@H](O)[C…`
ZINC4095713	0.583	342.3 Da LogP -5.40 TPSA 189.5	2 viol.	✓ Clean	`OC[C@H]1O[C@H](OC[C@H]2O[C@@](O)(CO)[C@@H](O)[C…`
ZINC4095714	0.583	342.3 Da LogP -5.40 TPSA 189.5	2 viol.	✓ Clean	`OC[C@H]1O[C@H](OC[C@H]2O[C@](O)(CO)[C@@H](O)[C@…`
ZINC64219256	0.583	342.3 Da LogP -5.40 TPSA 189.5	2 viol.	✓ Clean	`OC[C@@H]1O[C@H](OC[C@H]2O[C@@](O)(CO)[C@@H](O)[…`
ZINC64219257	0.583	342.3 Da LogP -5.40 TPSA 189.5	2 viol.	✓ Clean	`OC[C@H]1O[C@H](OC[C@@H]2O[C@@](O)(CO)[C@@H](O)[…`
ZINC64219258	0.583	342.3 Da LogP -5.40 TPSA 189.5	2 viol.	✓ Clean	`OC[C@@H]1O[C@H](OC[C@@H]2O[C@@](O)(CO)[C@@H](O)…`
ZINC12501558	0.563	276.1 Da LogP -3.38 TPSA 185.0	1 viol.	✓ Clean	`O=C(O)[C@H](O)[C@H](O)[C@H](O)[C@@H](O)COP(=O)(…`
ZINC12501560	0.563	276.1 Da LogP -3.38 TPSA 185.0	1 viol.	✓ Clean	`O=C(O)[C@H](O)[C@H](O)[C@H](O)[C@H](O)COP(=O)(O…`
ZINC12501562	0.563	276.1 Da LogP -3.38 TPSA 185.0	1 viol.	✓ Clean	`O=C(O)[C@H](O)[C@H](O)[C@@H](O)[C@@H](O)COP(=O)…`
ZINC12501564	0.563	276.1 Da LogP -3.38 TPSA 185.0	1 viol.	✓ Clean	`O=C(O)[C@H](O)[C@H](O)[C@@H](O)[C@H](O)COP(=O)(…`
ZINC1532623	0.563	276.1 Da LogP -3.38 TPSA 185.0	1 viol.	✓ Clean	`O=C(O)[C@H](O)[C@@H](O)[C@H](O)[C@H](O)COP(=O)(…`
ZINC2047359	0.563	276.1 Da LogP -3.38 TPSA 185.0	1 viol.	✓ Clean	`O=C(O)[C@@H](O)[C@@H](O)[C@H](O)[C@@H](O)COP(=O…`
ZINC2545091	0.563	276.1 Da LogP -3.38 TPSA 185.0	1 viol.	✓ Clean	`O=C(O)[C@@H](O)[C@H](O)[C@@H](O)[C@@H](O)COP(=O…`
ZINC3869602	0.563	276.1 Da LogP -3.38 TPSA 185.0	1 viol.	✓ Clean	`O=C(O)[C@@H](O)[C@@H](O)[C@@H](O)[C@@H](O)COP(=…`
ZINC3869603	0.563	276.1 Da LogP -3.38 TPSA 185.0	1 viol.	✓ Clean	`O=C(O)[C@@H](O)[C@@H](O)[C@@H](O)[C@H](O)COP(=O…`
ZINC3869604	0.563	276.1 Da LogP -3.38 TPSA 185.0	1 viol.	✓ Clean	`O=C(O)[C@@H](O)[C@@H](O)[C@H](O)[C@H](O)COP(=O)…`
ZINC100351924	0.559	260.1 Da LogP -3.10 TPSA 156.9	1 viol.	✓ Clean	`O=P(O)(O)OC[C@@H]1O[C@](O)(CO)[C@@H](O)[C@H]1O`
ZINC105102137	0.559	247.3 Da LogP -1.73 TPSA 93.4	✓ Ro5	✓ Clean	`OC[C@@H]1O[C@](O)(CN2CCCCC2)[C@@H](O)[C@H]1O`
ZINC105102147	0.559	247.3 Da LogP -1.73 TPSA 93.4	✓ Ro5	✓ Clean	`OC[C@@H]1O[C@](O)(CN2CCCCC2)[C@H](O)[C@H]1O`
ZINC12504372	0.559	260.1 Da LogP -3.10 TPSA 156.9	1 viol.	✓ Clean	`O=P(O)(O)OC[C@@H]1O[C@](O)(CO)[C@@H](O)[C@@H]1O`
ZINC1532847	0.559	260.1 Da LogP -3.10 TPSA 156.9	1 viol.	✓ Clean	`O=P(O)(O)OC[C@@H]1O[C@](O)(CO)[C@H](O)[C@@H]1O`
ZINC1719118	0.559	247.3 Da LogP -1.73 TPSA 93.4	✓ Ro5	✓ Clean	`OC[C@@H]1O[C@](O)(CN2CCCCC2)[C@H](O)[C@@H]1O`
ZINC3869919	0.559	260.1 Da LogP -3.10 TPSA 156.9	1 viol.	✓ Clean	`O=P(O)(O)OC[C@H]1O[C@@](O)(CO)[C@@H](O)[C@@H]1O`
ZINC4095539	0.559	260.1 Da LogP -3.10 TPSA 156.9	1 viol.	✓ Clean	`O=P(O)(O)OC[C@@]1(O)O[C@H](CO)[C@@H](O)[C@@H]1O`
ZINC4096690	0.559	260.1 Da LogP -3.10 TPSA 156.9	1 viol.	✓ Clean	`O=P(O)(O)OC[C@H]1O[C@](O)(CO)[C@@H](O)[C@@H]1O`
ZINC4896145	0.559	247.3 Da LogP -1.73 TPSA 93.4	✓ Ro5	✓ Clean	`OC[C@@H]1O[C@](O)(CN2CCCCC2)[C@@H](O)[C@@H]1O`
ZINC56874962	0.559	260.1 Da LogP -3.10 TPSA 156.9	1 viol.	✓ Clean	`O=P(O)(O)OC[C@H]1O[C@](O)(CO)[C@H](O)[C@@H]1O`

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.