Protein profile

VK055_2512

L-ribulokinase

Genome: KpATCC43816

Gene: AIK81109.1 araB Structure source: AlphaFold + ColabFold UniProt A0A0H3GJ58

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Amino acids 569

Annotations 8

Features 16

PDB binders 3

Druggability 0.818

Overview

Basic information about this protein and its source genome.

Accession: VK055_2512
Assembly: Klebsiella pneumoniae subsp. pneumoniae strain ATCC 43816 KPPR1, complete genome
Gene: AIK81109.1 araB
Status: annotated
Amino acids: 569
Structure source: AlphaFold + ColabFold

2.7.1.16

GO:0005524 Binding to ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator. GO:0008741 Catalysis of the reaction: ATP + L(or D)-ribulose = ADP + L(or D)-ribulose 5-phosphate. GO:0016301 Catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule. GO:0019569 The chemical reactions and pathways resulting in the breakdown of L-arabinose into D-xylulose 5-phosphate. 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:0005737 The contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

Target profile

Computed evidence for target prioritization.

Human off-target: hit
Human identity (%): 25.362
Human E-value: 2.53e-20
Gut microbiome off-target: hit
Essential (DEG): N
DEG identity (%): 28.025
Localization: Cytoplasmic
ColabFold pLDDT: 94.48

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 0.818

Structure A0A0H3GJ58

Pocket Pocket 7

P2Rank 0.967

Structure A0A0H3GJ58

Pocket Pocket 1

ColabFold model

FPocket 0.858 · Pocket 10

P2Rank 0.964 · Pocket 1

Core conservation Conserved core gene

Roary core

CoreCruncher core

Gut microbiome 144 / 4744 genomes with a hit

Normalized 0.03

Sequence

Primary amino-acid sequence viewer.

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 7 GO

Enzyme Commission (EC)

2.7.1.16

Gene Ontology (GO)

GO:0005524 Binding to ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
GO:0008741 Catalysis of the reaction: ATP + L(or D)-ribulose = ADP + L(or D)-ribulose 5-phosphate.
GO:0016301 Catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule.
GO:0019569 The chemical reactions and pathways resulting in the breakdown of L-arabinose into D-xylulose 5-phosphate.
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:0005737 The contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
GO:0019150 Catalysis of the reaction: ATP + D-ribulose = ADP + D-ribulose 5-phosphate.

Sequence Features

Domain/signature hits from InterPro and related databases.

16 records

Show feature table

Start	End	DB	Term	Name
2	514	CDD	cd07781	FGGY_RBK
2	514	InterPro	IPR005929	Ribulokinase
5	284	SUPERFAMILY	SSF53067	Actin-like ATPase domain
5	284	InterPro	IPR043129	ATPase, nucleotide binding domain
336	536	Gene3D	G3DSA:1.20.58.2240	-
353	373	Coils	Coil	Coil
2	550	NCBIfam	TIGR01234	ribulokinase
2	550	InterPro	IPR005929	Ribulokinase
5	526	Gene3D	G3DSA:3.30.420.40	-
1	558	Hamap	MF_00520	Ribulokinase [araB].
1	558	InterPro	IPR005929	Ribulokinase
291	501	Pfam	PF02782	FGGY family of carbohydrate kinases, C-terminal domain
291	501	InterPro	IPR018485	Carbohydrate kinase, FGGY, C-terminal
3	547	PANTHER	PTHR43435	RIBULOKINASE
285	542	SUPERFAMILY	SSF53067	Actin-like ATPase domain
285	542	InterPro	IPR043129	ATPase, nucleotide binding domain

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_A0A0H3GJ58	AlphaFold	—	—	full sequence	—	Viewing
ColabFold VK055_2512	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
7				0.818
26				0.454

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	30.3	0.934
2	3.24	0.112
3	1.78	0.033
4	1.75	0.032
5	1.61	0.026

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
10				0.858

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	28.88	0.928
2	2.82	0.088
3	1.87	0.037
4	1.74	0.031
5	1.29	0.013

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.

27 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
BTB	3GG4	Q665C6	209.2 Da LogP -3.01 TPSA 104.4	✓ Ro5	✓ Clean	`C(CO)N(CCO)C(CO)(CO)CO`
QDK	3QDK	Q9KBQ3	150.1 Da LogP -2.74 TPSA 98.0	✓ Ro5	✓ Clean	`C([C@@H]([C@@H](C(=O)CO)O)O)O`
XUL	3L0Q	Q665C6	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
ZINC1615342	1.000	209.2 Da LogP -3.01 TPSA 104.4	✓ Ro5	✓ Clean	`OCCN(CCO)C(CO)(CO)CO`
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`
ZINC2334905	0.522	261.4 Da LogP 1.10 TPSA 63.9	✓ Ro5	✓ Clean	`CC(C)CCN(CCC(C)C)C(CO)(CO)CO`
ZINC3159953	0.522	261.4 Da LogP 1.38 TPSA 63.9	✓ Ro5	✓ Clean	`CCCCCN(CCCCC)C(CO)(CO)CO`
ZINC113364020	0.500	330.5 Da LogP 3.75 TPSA 77.8	✓ Ro5	✓ Clean	`CCCCCCCCCCCCCCCC(=O)[C@@H](O)[C@@H](O)CO`
ZINC113364022	0.500	330.5 Da LogP 3.75 TPSA 77.8	✓ Ro5	✓ Clean	`CCCCCCCCCCCCCCCC(=O)[C@H](O)[C@@H](O)CO`
ZINC113364024	0.500	330.5 Da LogP 3.75 TPSA 77.8	✓ Ro5	✓ Clean	`CCCCCCCCCCCCCCCC(=O)[C@@H](O)[C@H](O)CO`
ZINC113364025	0.500	330.5 Da LogP 3.75 TPSA 77.8	✓ Ro5	✓ Clean	`CCCCCCCCCCCCCCCC(=O)[C@H](O)[C@H](O)CO`
ZINC1529626	0.500	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	0.500	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	0.500	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	0.500	230.1 Da LogP -2.62 TPSA 144.5	✓ Ro5	✓ Clean	`O=C(CO)[C@@H](O)[C@H](O)COP(=O)(O)O`
ZINC31259596	0.500	230.1 Da LogP -2.62 TPSA 144.5	✓ Ro5	✓ Clean	`O=C(COP(=O)(O)O)[C@@H](O)[C@H](O)CO`
ZINC31259600	0.500	230.1 Da LogP -2.62 TPSA 144.5	✓ Ro5	✓ Clean	`O=C(COP(=O)(O)O)[C@@H](O)[C@@H](O)CO`
ZINC3869804	0.500	230.1 Da LogP -2.62 TPSA 144.5	✓ Ro5	✓ Clean	`O=C(COP(=O)(O)O)[C@H](O)[C@@H](O)CO`
ZINC3869805	0.500	230.1 Da LogP -2.62 TPSA 144.5	✓ Ro5	✓ Clean	`O=C(COP(=O)(O)O)[C@H](O)[C@H](O)CO`
ZINC5297554	0.500	289.5 Da LogP 2.16 TPSA 63.9	✓ Ro5	✓ Clean	`CCCCCCN(CCCCCC)C(CO)(CO)CO`
ZINC97941822	0.500	317.5 Da LogP 2.94 TPSA 63.9	✓ Ro5	✓ Clean	`CCCCCCCN(CCCCCCC)C(CO)(CO)CO`
ZINC97942927	0.500	373.6 Da LogP 4.51 TPSA 63.9	✓ Ro5	✓ Clean	`CCCCCCCCCN(CCCCCCCCC)C(CO)(CO)CO`

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.