Protein profile

VK055_0446

pfkB carbohydrate kinase family protein

Genome: KpATCC43816

Gene: AIK79072.1 Structure source: AlphaFold + ColabFold UniProt A0A0C7KN58

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Amino acids 308

Annotations 8

Features 25

PDB binders 8

Druggability 0.15

Overview

Basic information about this protein and its source genome.

Accession: VK055_0446
Assembly: Klebsiella pneumoniae subsp. pneumoniae strain ATCC 43816 KPPR1, complete genome
Gene: AIK79072.1
Status: annotated
Amino acids: 308
Structure source: AlphaFold + ColabFold

2.7.1.15

GO:0016301 Catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule. GO:0006014 The chemical reactions and pathways involving D-ribose (ribo-pentose). As beta-D-ribofuranose, D-ribose forms the glycose group of all ribonucleosides, ribonucleotides and ribonucleic acids, and also of ribose phosphates, various glycosides, some coenzymes and some forms of vitamin B12. GO:0004747 Catalysis of the reaction: ATP + D-ribose = ADP + D-ribose 5-phosphate. GO:0005737 The contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures. GO:0005524 Binding to ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator. GO:0046872 Binding to a metal ion.

Target profile

Computed evidence for target prioritization.

Human off-target: hit
Human identity (%): 35.43
Human E-value: 1.1399999999999999e-40
Gut microbiome off-target: No hit
Essential (DEG): N
DEG identity (%): 36.577
Localization: Cytoplasmic
ColabFold pLDDT: 94.54

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 0.15

Structure A0A0C7KN58

Pocket Pocket 10

P2Rank 0.969

Structure A0A0C7KN58

Pocket Pocket 1

ColabFold model

FPocket 0.35 · Pocket 9

P2Rank 0.971 · Pocket 1

Core conservation Accessory gene

Roary accessory

CoreCruncher accessory

Gut microbiome 0 / 4744 genomes with a hit

Normalized 0

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)

2.7.1.15

Gene Ontology (GO)

GO:0016301 Catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule.
GO:0006014 The chemical reactions and pathways involving D-ribose (ribo-pentose). As beta-D-ribofuranose, D-ribose forms the glycose group of all ribonucleosides, ribonucleotides and ribonucleic acids, and also of ribose phosphates, various glycosides, some coenzymes and some forms of vitamin B12.
GO:0004747 Catalysis of the reaction: ATP + D-ribose = ADP + D-ribose 5-phosphate.
GO:0005737 The contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
GO:0005524 Binding to ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
GO:0046872 Binding to a metal ion.
GO:0019303 The chemical reactions and pathways resulting in the breakdown of D-ribose (ribo-pentose).

Sequence Features

Domain/signature hits from InterPro and related databases.

25 records

Show feature table

Start	End	DB	Term	Name
39	63	ProSitePatterns	PS00583	pfkB family of carbohydrate kinases signature 1.
39	63	InterPro	IPR002173	Carbohydrate/purine kinase, PfkB, conserved site
4	292	CDD	cd01174	ribokinase
4	292	InterPro	IPR011877	Ribokinase
3	292	Pfam	PF00294	pfkB family carbohydrate kinase
3	292	InterPro	IPR011611	Carbohydrate kinase PfkB
1	305	Gene3D	G3DSA:3.40.1190.20	-
1	305	InterPro	IPR029056	Ribokinase-like
3	299	Hamap	MF_01987	Ribokinase [rbsK].
3	299	InterPro	IPR011877	Ribokinase
5	302	PANTHER	PTHR10584	SUGAR KINASE
245	258	ProSitePatterns	PS00584	pfkB family of carbohydrate kinases signature 2.
245	258	InterPro	IPR002173	Carbohydrate/purine kinase, PfkB, conserved site
1	294	SUPERFAMILY	SSF53613	Ribokinase-like
1	294	InterPro	IPR029056	Ribokinase-like
105	118	PRINTS	PR00990	Ribokinase signature
105	118	InterPro	IPR002139	Ribokinase/fructokinase
171	186	PRINTS	PR00990	Ribokinase signature
171	186	InterPro	IPR002139	Ribokinase/fructokinase
7	28	PRINTS	PR00990	Ribokinase signature
7	28	InterPro	IPR002139	Ribokinase/fructokinase
215	226	PRINTS	PR00990	Ribokinase signature
215	226	InterPro	IPR002139	Ribokinase/fructokinase
34	53	PRINTS	PR00990	Ribokinase signature
34	53	InterPro	IPR002139	Ribokinase/fructokinase

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_A0A0C7KN58	AlphaFold	—	—	full sequence	—	Viewing
ColabFold VK055_0446	ColabFold	—	—	full sequence	—	Loaded

Pocket details FPocket · P2Rank — toggle visibility and zoom from here, or open full viewer

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				28.04	0.923
2				0.66	0.001

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
9				0.35

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				30.87	0.936

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.

58 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
A12	6WJZ	Q9H477	425.2 Da LogP -1.64 TPSA 223.4	2 viol.	✓ Clean	`c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)…`
ACP	6A8B	A0A3S7X0F5	505.2 Da LogP -1.52 TPSA 269.9	3 viol.	✓ Clean	`c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)…`
AN2	5C3Y	Q9H477	426.2 Da LogP -1.78 TPSA 238.4	2 viol.	✓ Clean	`c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)…`
ANP	3IH0	O59128	506.2 Da LogP -2.06 TPSA 281.9	3 viol.	✓ Clean	`c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)…`
MZR	3B1N	Q2SZE4	259.2 Da LogP -2.70 TPSA 151.1	✓ Ro5	✓ Clean	`c1nc(c(n1[C@H]2[C@@H]([C@@H]([C@H](O2)CO)O)O)O)…`
NOS	3B1P	Q2SZE4	268.2 Da LogP -2.27 TPSA 133.5	✓ Ro5	✓ Clean	`c1nc2c(n1[C@H]3[C@@H]([C@@H]([C@H](O3)CO)O)O)N=…`
P33	3B1Q	Q2SZE4	326.4 Da LogP -0.93 TPSA 95.8	✓ Ro5	✓ Clean	`C(COCCOCCOCCOCCOCCOCCO)O`
RIB	6ILS	A1A6H3	150.1 Da LogP -2.58 TPSA 90.2	✓ Ro5	✓ Clean	`C([C@@H]1[C@H]([C@H]([C@H](O1)O)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
ZINC11616261	1.000	259.2 Da LogP -2.70 TPSA 151.1	✓ Ro5	✓ Clean	`NC(=O)c1ncn([C@@H]2O[C@H](CO)[C@@H](O)[C@@H]2O)…`
ZINC12501520	1.000	458.5 Da LogP -0.88 TPSA 123.5	1 viol.	✓ Clean	`OCCOCCOCCOCCOCCOCCOCCOCCOCCOCCO`
ZINC1542903	1.000	259.2 Da LogP -2.70 TPSA 151.1	✓ Ro5	✓ Clean	`NC(=O)c1ncn([C@H]2O[C@@H](CO)[C@H](O)[C@@H]2O)c…`
ZINC16951611	1.000	268.2 Da LogP -2.27 TPSA 133.5	✓ Ro5	✓ Clean	`O=c1[nH]cnc2c1ncn2[C@H]1O[C@@H](CO)[C@H](O)[C@H…`
ZINC2573068	1.000	268.2 Da LogP -2.27 TPSA 133.5	✓ Ro5	✓ Clean	`O=c1[nH]cnc2c1ncn2[C@@H]1O[C@@H](CO)[C@H](O)[C@…`
ZINC3812887	1.000	259.2 Da LogP -2.70 TPSA 151.1	✓ Ro5	✓ Clean	`NC(=O)c1ncn([C@@H]2O[C@H](CO)[C@@H](O)[C@H]2O)c…`
ZINC3874716	1.000	414.5 Da LogP -0.90 TPSA 114.3	✓ Ro5	✓ Clean	`OCCOCCOCCOCCOCCOCCOCCOCCOCCO`
ZINC3978085	1.000	259.2 Da LogP -2.70 TPSA 151.1	✓ Ro5	✓ Clean	`NC(=O)c1ncn([C@@H]2O[C@H](CO)[C@H](O)[C@@H]2O)c…`
ZINC4015531	1.000	268.2 Da LogP -2.27 TPSA 133.5	✓ Ro5	✓ Clean	`O=c1[nH]cnc2c1ncn2[C@@H]1O[C@@H](CO)[C@@H](O)[C…`
ZINC4283769	1.000	238.3 Da LogP -0.96 TPSA 77.4	✓ Ro5	✓ Clean	`OCCOCCOCCOCCOCCO`
ZINC4521548	1.000	282.3 Da LogP -0.95 TPSA 86.6	✓ Ro5	✓ Clean	`OCCOCCOCCOCCOCCOCCO`
ZINC5127789	1.000	268.2 Da LogP -2.27 TPSA 133.5	✓ Ro5	✓ Clean	`O=c1[nH]cnc2c1ncn2[C@H]1O[C@H](CO)[C@@H](O)[C@H…`
ZINC5178829	1.000	326.4 Da LogP -0.93 TPSA 95.8	✓ Ro5	✓ Clean	`OCCOCCOCCOCCOCCOCCOCCO`
ZINC5178830	1.000	370.4 Da LogP -0.91 TPSA 105.1	✓ Ro5	✓ Clean	`OCCOCCOCCOCCOCCOCCOCCOCCO`
ZINC67665203	1.000	259.2 Da LogP -2.70 TPSA 151.1	✓ Ro5	✓ Clean	`NC(=O)c1ncn([C@@H]2O[C@H](CO)[C@H](O)[C@H]2O)c1O`
ZINC8613160	1.000	268.2 Da LogP -2.27 TPSA 133.5	✓ Ro5	✓ Clean	`O=c1[nH]cnc2c1ncn2[C@@H]1O[C@H](CO)[C@H](O)[C@@…`
ZINC8613161	1.000	268.2 Da LogP -2.27 TPSA 133.5	✓ Ro5	✓ Clean	`O=c1[nH]cnc2c1ncn2[C@@H]1O[C@H](CO)[C@H](O)[C@H…`
ZINC8614390	1.000	268.2 Da LogP -2.27 TPSA 133.5	✓ Ro5	✓ Clean	`O=c1[nH]cnc2c1ncn2[C@@H]1O[C@@H](CO)[C@@H](O)[C…`
ZINC8652273	1.000	268.2 Da LogP -2.27 TPSA 133.5	✓ Ro5	✓ Clean	`O=c1[nH]cnc2c1ncn2[C@H]1O[C@@H](CO)[C@@H](O)[C@…`
ZINC8652274	1.000	268.2 Da LogP -2.27 TPSA 133.5	✓ Ro5	✓ Clean	`O=c1[nH]cnc2c1ncn2[C@H]1O[C@@H](CO)[C@@H](O)[C@…`
ZINC8855117	1.000	268.2 Da LogP -2.27 TPSA 133.5	✓ Ro5	✓ Clean	`O=c1[nH]cnc2c1ncn2[C@@H]1O[C@H](CO)[C@@H](O)[C@…`
ZINC895160	1.000	268.2 Da LogP -2.27 TPSA 133.5	✓ Ro5	✓ Clean	`O=c1[nH]cnc2c1ncn2[C@H]1O[C@@H](CO)[C@H](O)[C@@…`
ZINC219330894	0.873	425.2 Da LogP -1.64 TPSA 223.4	2 viol.	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@H](CO[P@](=O)(O)CP(=O)…`
ZINC106381023	0.826	267.2 Da LogP -2.30 TPSA 139.3	✓ Ro5	✓ Clean	`N[C@H]1[C@H](O)[C@@H](CO)O[C@H]1n1cnc2c(=O)[nH]…`
ZINC31542954	0.826	267.2 Da LogP -2.30 TPSA 139.3	✓ Ro5	✓ Clean	`N[C@@H]1[C@H](O)[C@@H](CO)O[C@H]1n1cnc2c(=O)[nH…`
ZINC31543351	0.826	270.2 Da LogP -1.29 TPSA 113.3	✓ Ro5	✓ Clean	`O=c1[nH]cnc2c1ncn2[C@@H]1O[C@H](CO)[C@@H](O)[C@…`
ZINC3645702	0.826	267.2 Da LogP -2.30 TPSA 139.3	✓ Ro5	✓ Clean	`N[C@@H]1[C@@H](n2cnc3c(=O)[nH]cnc32)O[C@@H](CO)…`
ZINC4634665	0.826	270.2 Da LogP -1.29 TPSA 113.3	✓ Ro5	✓ Clean	`O=c1[nH]cnc2c1ncn2[C@@H]1O[C@H](CO)[C@@H](O)[C@…`
ZINC5106288	0.818	270.2 Da LogP -1.29 TPSA 113.3	✓ Ro5	✓ Clean	`O=c1[nH]cnc2c1ncn2[C@H]1O[C@@H](CF)[C@@H](O)[C@…`
ZINC5106290	0.818	270.2 Da LogP -1.29 TPSA 113.3	✓ Ro5	✓ Clean	`O=c1[nH]cnc2c1ncn2[C@@H]1O[C@@H](CF)[C@@H](O)[C…`
ZINC5106293	0.818	270.2 Da LogP -1.29 TPSA 113.3	✓ Ro5	✓ Clean	`O=c1[nH]cnc2c1ncn2[C@H]1O[C@@H](CF)[C@@H](O)[C@…`
ZINC5106295	0.818	270.2 Da LogP -1.29 TPSA 113.3	✓ Ro5	✓ Clean	`O=c1[nH]cnc2c1ncn2[C@@H]1O[C@@H](CF)[C@@H](O)[C…`
ZINC4963541	0.787	281.3 Da LogP -2.04 TPSA 125.3	✓ Ro5	✓ Clean	`CN[C@@H]1[C@H](CO)O[C@H](n2cnc3c(=O)[nH]cnc32)[…`
ZINC4963542	0.787	281.3 Da LogP -2.04 TPSA 125.3	✓ Ro5	✓ Clean	`CN[C@H]1[C@H](CO)O[C@H](n2cnc3c(=O)[nH]cnc32)[C…`
ZINC4963543	0.787	281.3 Da LogP -2.04 TPSA 125.3	✓ Ro5	✓ Clean	`CN[C@@H]1[C@@H](CO)O[C@H](n2cnc3c(=O)[nH]cnc32)…`
ZINC4963544	0.787	281.3 Da LogP -2.04 TPSA 125.3	✓ Ro5	✓ Clean	`CN[C@H]1[C@@H](CO)O[C@H](n2cnc3c(=O)[nH]cnc32)[…`
ZINC110928985	0.776	282.3 Da LogP -1.61 TPSA 122.5	✓ Ro5	✓ Clean	`CO[C@H]1[C@@H](O)[C@@H](CO)O[C@H]1n1cnc2c(=O)[n…`
ZINC110928990	0.776	282.3 Da LogP -1.61 TPSA 122.5	✓ Ro5	✓ Clean	`CO[C@H]1[C@H](O)[C@@H](CO)O[C@H]1n1cnc2c(=O)[nH…`
ZINC34149906	0.776	282.3 Da LogP -1.61 TPSA 122.5	✓ Ro5	✓ Clean	`CO[C@@H]1[C@H](O)[C@@H](CO)O[C@H]1n1cnc2c(=O)[n…`
ZINC11616872	0.762	258.2 Da LogP -2.82 TPSA 156.9	✓ Ro5	✓ Clean	`NC(=O)c1ncn([C@H]2O[C@H](CO)[C@@H](O)[C@@H]2O)c…`
ZINC13547762	0.762	258.2 Da LogP -2.82 TPSA 156.9	✓ Ro5	✓ Clean	`NC(=O)c1ncn([C@@H]2O[C@H](CO)[C@H](O)[C@H]2O)c1N`
ZINC198950922	0.762	258.2 Da LogP -2.82 TPSA 156.9	✓ Ro5	✓ Clean	`NC(=O)c1ncn([C@H]2O[C@@H](CO)[C@H](O)[C@@H]2O)c…`
ZINC3798074	0.762	258.2 Da LogP -2.82 TPSA 156.9	✓ Ro5	✓ Clean	`NC(=O)c1ncn([C@@H]2O[C@H](CO)[C@@H](O)[C@H]2O)c…`
ZINC44184441	0.762	258.2 Da LogP -2.82 TPSA 156.9	✓ Ro5	✓ Clean	`NC(=O)c1ncn([C@@H]2O[C@H](CO)[C@H](O)[C@@H]2O)c…`
ZINC4772258	0.762	286.2 Da LogP -3.31 TPSA 173.9	✓ Ro5	✓ Clean	`NC(=O)c1ncn([C@H]2O[C@@H](CO)[C@@H](O)[C@H]2O)c…`
ZINC4772259	0.762	286.2 Da LogP -3.31 TPSA 173.9	✓ Ro5	✓ Clean	`NC(=O)c1ncn([C@@H]2O[C@@H](CO)[C@@H](O)[C@H]2O)…`
ZINC4877289	0.762	258.2 Da LogP -2.82 TPSA 156.9	✓ Ro5	✓ Clean	`NC(=O)c1ncn([C@H]2O[C@@H](CO)[C@@H](O)[C@H]2O)c…`
ZINC4877292	0.762	258.2 Da LogP -2.82 TPSA 156.9	✓ Ro5	✓ Clean	`NC(=O)c1ncn([C@H]2O[C@@H](CO)[C@@H](O)[C@@H]2O)…`
ZINC4877294	0.762	258.2 Da LogP -2.82 TPSA 156.9	✓ Ro5	✓ Clean	`NC(=O)c1ncn([C@@H]2O[C@@H](CO)[C@@H](O)[C@@H]2O…`
ZINC669678934	0.762	258.2 Da LogP -2.82 TPSA 156.9	✓ Ro5	✓ Clean	`NC(=O)c1ncn([C@H]2O[C@@H](CO)[C@H](O)[C@H]2O)c1N`

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.