Protein profile

KP13_03421

Glycerol kinase

Genome: KpKP13

Gene: AHE45798.1 Structure source: AlphaFold + ColabFold UniProt A0A486INR3

Export view

Amino acids 499

Annotations 7

Features 17

PDB binders 13

Druggability 0.694

Overview

Basic information about this protein and its source genome.

Accession: KP13_03421
Assembly: Klebsiella pneumoniae subsp. pneumoniae Kp13, complete sequence
Gene: AHE45798.1
Status: annotated
Amino acids: 499
Structure source: AlphaFold + ColabFold

GO:0016773 Catalysis of the transfer of a phosphorus-containing group from one compound (donor) to an alcohol group (acceptor). 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: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+.

Target profile

Computed evidence for target prioritization.

Human off-target: hit
Human identity (%): 34.667
Human E-value: 8.22e-85
Gut microbiome off-target: hit
Essential (DEG): Y
DEG identity (%): 41.304
DEG E-value: 8.19e-98
Localization: Cytoplasmic
ColabFold pLDDT: 95.45

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 0.694

Structure A0A486INR3

Pocket Pocket 16

P2Rank 0.924

Structure A0A486INR3

Pocket Pocket 1

ColabFold model

FPocket 0.735 · Pocket 17

P2Rank 0.977 · Pocket 1

Core conservation Accessory gene

Roary accessory

CoreCruncher accessory

Gut microbiome 29 / 4744 genomes with a hit

Normalized 0.006

Sequence

Primary amino-acid sequence viewer.

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

7 GO

Gene Ontology (GO)

GO:0016773 Catalysis of the transfer of a phosphorus-containing group from one compound (donor) to an alcohol group (acceptor).
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: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:0019563 The chemical reactions and pathways resulting in the breakdown of 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.

17 records

Show feature table

Start	End	DB	Term	Name
3	252	Gene3D	G3DSA:3.30.420.40	-
366	386	ProSitePatterns	PS00445	FGGY family of carbohydrate kinases signature 2.
366	386	InterPro	IPR018483	Carbohydrate kinase, FGGY, conserved site
5	499	PIRSF	PIRSF000538	GlpK
5	499	InterPro	IPR000577	Carbohydrate kinase, FGGY
8	495	PANTHER	PTHR10196	SUGAR KINASE
257	498	Gene3D	G3DSA:3.30.420.40	-
257	493	SUPERFAMILY	SSF53067	Actin-like ATPase domain
257	493	InterPro	IPR043129	ATPase, nucleotide binding domain
262	454	Pfam	PF02782	FGGY family of carbohydrate kinases, C-terminal domain
262	454	InterPro	IPR018485	Carbohydrate kinase, FGGY, C-terminal
7	254	SUPERFAMILY	SSF53067	Actin-like ATPase domain
7	254	InterPro	IPR043129	ATPase, nucleotide binding domain
7	498	CDD	cd07791	FGGY_GK2_bacteria
7	498	InterPro	IPR042016	Apulose kinase
7	251	Pfam	PF00370	FGGY family of carbohydrate kinases, N-terminal domain
7	251	InterPro	IPR018484	Carbohydrate kinase, FGGY, N-terminal

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...

Legend High Medium Low

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_A0A486INR3	AlphaFold	—	—	full sequence	—	Viewing
ColabFold KP13_03421	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
16				0.694

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	20.63	0.859
2	2.48	0.068
3	2.16	0.051
4	1.99	0.043
5	1.21	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
17				0.735

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	35.08	0.952
2	2.68	0.079
3	2.48	0.068
4	1.59	0.025
5	1.02	0.006

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.

63 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
4NP	5AZI	D3KVM3	219.1 Da LogP 1.07 TPSA 109.9	✓ Ro5	✓ Clean	`c1cc(ccc1[N+](=O)[O-])OP(=O)(O)O`
6XZ	5GN5	D3KVM3	382.4 Da LogP 2.54 TPSA 86.4	✓ Ro5	Alert	`COc1ccc(cc1)N2CCN(CC2)CC3=CC(=O)Oc4c3ccc(c4O)O`
6Y0	5GN6	D3KVM3	234.3 Da LogP 2.55 TPSA 70.7	✓ Ro5	Alert	`CCCCC1=CC(=O)Oc2c1ccc(c2O)O`
ACP	1GLL	P0A6F3	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)…`
ANP	6J9Q	D3KVM3	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)…`
ATF	1BWF	P0A6F3	541.2 Da LogP -0.93 TPSA 269.9	3 viol.	✓ Clean	`c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)…`
ATS	1GLJ	P0A6F3	549.2 Da LogP -2.76 TPSA 269.9	3 viol.	✓ Clean	`c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)…`
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`
G3H	1GLC	P0A6F3	170.1 Da LogP -1.34 TPSA 104.1	✓ Ro5	✓ Clean	`C([C@H](C=O)O)OP(=O)(O)O`
G3P	3WXJ	D3KVM3	172.1 Da LogP -1.55 TPSA 107.2	✓ Ro5	✓ Clean	`C([C@H](COP(=O)(O)O)O)O`
NH4	2ITM	P09099	18.0 Da LogP 0.38 TPSA 36.5	✓ Ro5	✓ Clean	`[NH4+]`
POP	6JAF	D3KVM3	176.0 Da LogP -2.08 TPSA 129.9	✓ Ro5	✓ Clean	`O[P@@](=O)([O-])O[P@@](=O)(O)[O-]`
XUL	2ITM	P09099	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
ZINC1529638	1.000	219.1 Da LogP 1.07 TPSA 109.9	✓ Ro5	✓ Clean	`O=[N+]([O-])c1ccc(OP(=O)(O)O)cc1`
ZINC2865681	1.000	234.3 Da LogP 2.55 TPSA 70.7	✓ Ro5	Alert	`CCCCc1cc(=O)oc2c(O)c(O)ccc12`
ZINC54219977	1.000	382.4 Da LogP 2.54 TPSA 86.4	✓ Ro5	Alert	`COc1ccc(N2CCN(Cc3cc(=O)oc4c(O)c(O)ccc34)CC2)cc1`
ZINC105469665	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…`
ZINC13527614	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)…`
ZINC3873852	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)…`
ZINC3873853	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…`
ZINC3873854	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)…`
ZINC3873855	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…`
ZINC12360002	0.839	427.2 Da LogP -1.75 TPSA 232.6	2 viol.	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@H](CO[P@@](=O)(O)OP(=O…`
ZINC12360703	0.839	427.2 Da LogP -1.75 TPSA 232.6	2 viol.	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@H](CO[P@@](=O)(O)OP(=O…`
ZINC12503599	0.839	427.2 Da LogP -1.75 TPSA 232.6	2 viol.	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@H](CO[P@@](=O)(O)OP(=O…`
ZINC16546165	0.839	427.2 Da LogP -1.75 TPSA 232.6	2 viol.	✓ Clean	`Nc1ncnc2c1ncn2[C@H]1O[C@H](CO[P@](=O)(O)OP(=O)(…`
ZINC31977053	0.839	427.2 Da LogP -1.75 TPSA 232.6	2 viol.	✓ Clean	`Nc1ncnc2c1ncn2[C@H]1O[C@@H](CO[P@](=O)(O)OP(=O)…`
ZINC4806433	0.839	427.2 Da LogP -1.75 TPSA 232.6	2 viol.	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@H](CO[P@@](=O)(O)OP(=O…`
ZINC53683898	0.839	427.2 Da LogP -1.75 TPSA 232.6	2 viol.	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@@H](CO[P@@](=O)(O)OP(=…`
ZINC8586019	0.839	427.2 Da LogP -1.75 TPSA 232.6	2 viol.	✓ Clean	`Nc1ncnc2c1ncn2[C@H]1O[C@@H](CO[P@](=O)(O)OP(=O)…`
ZINC8586020	0.839	427.2 Da LogP -1.75 TPSA 232.6	2 viol.	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@@H](CO[P@@](=O)(O)OP(=…`
ZINC8586021	0.839	427.2 Da LogP -1.75 TPSA 232.6	2 viol.	✓ Clean	`Nc1ncnc2c1ncn2[C@H]1O[C@@H](CO[P@@](=O)(O)OP(=O…`
ZINC8586022	0.839	427.2 Da LogP -1.75 TPSA 232.6	2 viol.	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@@H](CO[P@@](=O)(O)OP(=…`
ZINC5547487	0.838	220.2 Da LogP 2.16 TPSA 70.7	✓ Ro5	Alert	`CCCc1cc(=O)oc2c(O)c(O)ccc12`
ZINC54105934	0.830	380.4 Da LogP 3.14 TPSA 66.2	✓ Ro5	Alert	`COc1ccc(N2CCN(Cc3cc(=O)oc4c(C)c(O)ccc34)CC2)cc1`
ZINC1529745	0.786	340.2 Da LogP 3.06 TPSA 142.0	✓ Ro5	✓ Clean	`O=[N+]([O-])c1ccc(OP(=O)(O)Oc2ccc([N+](=O)[O-])…`
ZINC1902771	0.775	232.3 Da LogP 3.15 TPSA 50.4	✓ Ro5	✓ Clean	`CCCCc1cc(=O)oc2c(C)c(O)ccc12`
ZINC13518964	0.768	347.2 Da LogP -1.86 TPSA 186.1	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@@H](COP(=O)(O)O)[C@H](…`
ZINC1532515	0.768	347.2 Da LogP -1.86 TPSA 186.1	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@H]1O[C@@H](COP(=O)(O)O)[C@H](O…`
ZINC1571045	0.768	347.2 Da LogP -1.86 TPSA 186.1	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@@H](COP(=O)(O)O)[C@@H]…`
ZINC1842158	0.768	347.2 Da LogP -1.86 TPSA 186.1	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@H]1O[C@@H](COP(=O)(O)O)[C@H](O…`
ZINC2046931	0.768	347.2 Da LogP -1.86 TPSA 186.1	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@@H](COP(=O)(O)O)[C@H](…`
ZINC2126310	0.768	347.2 Da LogP -1.86 TPSA 186.1	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@H](COP(=O)(O)O)[C@@H](…`
ZINC3201891	0.768	347.2 Da LogP -1.86 TPSA 186.1	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@@H](COP(=O)(O)O)[C@@H]…`
ZINC3201893	0.768	347.2 Da LogP -1.86 TPSA 186.1	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@H]1O[C@@H](COP(=O)(O)O)[C@@H](…`
ZINC3830180	0.768	347.2 Da LogP -1.86 TPSA 186.1	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@H]1O[C@@H](COP(=O)(O)O)[C@@H](…`
ZINC3860156	0.768	347.2 Da LogP -1.86 TPSA 186.1	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@H](COP(=O)(O)O)[C@@H](…`
ZINC3977897	0.768	347.2 Da LogP -1.86 TPSA 186.1	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@H]1O[C@H](COP(=O)(O)O)[C@@H](O…`
ZINC4806442	0.768	347.2 Da LogP -1.86 TPSA 186.1	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@H](COP(=O)(O)O)[C@H](O…`
ZINC8613167	0.768	347.2 Da LogP -1.86 TPSA 186.1	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@H](COP(=O)(O)O)[C@H](O…`
ZINC615051	0.757	206.2 Da LogP 1.77 TPSA 70.7	✓ Ro5	Alert	`CCc1cc(=O)oc2c(O)c(O)ccc12`
ZINC54147570	0.755	370.4 Da LogP 2.67 TPSA 77.2	✓ Ro5	Alert	`O=c1cc(CN2CCN(c3ccc(F)cc3)CC2)c2ccc(O)c(O)c2o1`
ZINC4096224	0.754	346.2 Da LogP -1.90 TPSA 191.9	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@H](CO[P@](N)(=O)O)[C@@…`
ZINC12503850	0.750	427.3 Da LogP -2.04 TPSA 229.4	1 viol.	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@H](CO[P@](=O)(O)OS(=O)…`
ZINC141161066	0.750	427.3 Da LogP -2.04 TPSA 229.4	1 viol.	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@H](CO[P@](=O)(O)OS(=O)…`
ZINC141163786	0.750	427.3 Da LogP -2.04 TPSA 229.4	1 viol.	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@H](CO[P@](=O)(O)OS(=O)…`
ZINC4228246	0.750	427.3 Da LogP -2.04 TPSA 229.4	1 viol.	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@H](CO[P@@](=O)(O)OS(=O…`
ZINC54147573	0.750	352.4 Da LogP 2.53 TPSA 77.2	✓ Ro5	Alert	`O=c1cc(CN2CCN(c3ccccc3)CC2)c2ccc(O)c(O)c2o1`
ZINC57435033	0.741	382.4 Da LogP 2.54 TPSA 86.4	✓ Ro5	Alert	`COc1ccc(N2CCN(Cc3cc(=O)oc4cc(O)c(O)cc34)CC2)cc1`
ZINC58451816	0.741	366.4 Da LogP 2.83 TPSA 66.2	✓ Ro5	Alert	`COc1ccc(N2CCN(Cc3cc(=O)oc4cc(O)ccc34)CC2)cc1`
ZINC105372837	0.737	345.3 Da LogP -1.93 TPSA 197.6	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@H](COP(N)(N)=O)[C@H](O…`
ZINC17107643	0.737	345.3 Da LogP -1.93 TPSA 197.6	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@H](COP(N)(N)=O)[C@@H](…`
ZINC204538551	0.737	345.3 Da LogP -1.93 TPSA 197.6	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@H](COP(N)(N)=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.