Protein profile

KP13_00949

Thiamine biosynthesis lipoprotein apbE

Genome: KpKP13

Gene: AHE43523.1 apbE Structure source: AlphaFold + ColabFold UniProt A0A0H3GSX9

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Amino acids 350

Annotations 5

Features 20

PDB binders 1

Druggability 0.49

Overview

Basic information about this protein and its source genome.

Accession: KP13_00949
Assembly: Klebsiella pneumoniae subsp. pneumoniae Kp13, complete sequence
Gene: AHE43523.1 apbE
Status: annotated
Amino acids: 350
Structure source: AlphaFold + ColabFold

2.7.1.180

GO:0017013 The addition of a flavin group to a protein amino acid. GO:0005886 The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins. GO:0046872 Binding to a metal ion. GO:0016740 Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2.

Target profile

Computed evidence for target prioritization.

Human off-target: No hit
Human identity (%): 0.0
Gut microbiome off-target: hit
Essential (DEG): Y
DEG identity (%): 41.214
DEG E-value: 5.09e-86
Localization: Unknown
ColabFold pLDDT: 89.84

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 0.49

Structure A0A0H3GSX9

Pocket Pocket 3

P2Rank 0.894

Structure A0A0H3GSX9

Pocket Pocket 1

ColabFold model

FPocket 0.61 · Pocket 5

P2Rank 0.837 · Pocket 1

Core conservation Conserved core gene

Roary core

CoreCruncher core

Gut microbiome 79 / 4744 genomes with a hit

Normalized 0.017

Sequence

Primary amino-acid sequence viewer.

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 4 GO

Enzyme Commission (EC)

2.7.1.180

Gene Ontology (GO)

GO:0017013 The addition of a flavin group to a protein amino acid.
GO:0005886 The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.
GO:0046872 Binding to a metal ion.
GO:0016740 Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2.

Sequence Features

Domain/signature hits from InterPro and related databases.

20 records

Show feature table

Start	End	DB	Term	Name
7	344	PANTHER	PTHR30040	THIAMINE BIOSYNTHESIS LIPOPROTEIN APBE
7	344	InterPro	IPR024932	Flavin transferase ApbE
1	23	SignalP_GRAM_NEGATIVE	SignalP-noTM	SignalP-noTM
1	7	Phobius	SIGNAL_PEPTIDE_N_REGION	N-terminal region of a signal peptide.
25	347	FunFam	G3DSA:3.10.520.10:FF:000001	FAD:protein FMN transferase
18	22	Phobius	SIGNAL_PEPTIDE_C_REGION	C-terminal region of a signal peptide.
8	17	Phobius	SIGNAL_PEPTIDE_H_REGION	Hydrophobic region of a signal peptide.
3	346	PIRSF	PIRSF006268	ApbE
3	346	InterPro	IPR024932	Flavin transferase ApbE
1	20	ProSiteProfiles	PS51257	Prokaryotic membrane lipoprotein lipid attachment site profile.
23	350	Phobius	NON_CYTOPLASMIC_DOMAIN	Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
22	350	Gene3D	G3DSA:3.10.520.10	-
22	350	InterPro	IPR003374	ApbE-like superfamily
1	22	SignalP_EUK	SignalP-noTM	SignalP-noTM
1	23	SignalP_GRAM_POSITIVE	SignalP-TM	SignalP-TM
41	324	Pfam	PF02424	ApbE family
41	324	InterPro	IPR024932	Flavin transferase ApbE
35	345	SUPERFAMILY	SSF143631	ApbE-like
35	345	InterPro	IPR003374	ApbE-like superfamily
1	22	Phobius	SIGNAL_PEPTIDE	Signal peptide region

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_A0A0H3GSX9	AlphaFold	—	—	full sequence	—	Viewing
ColabFold KP13_00949	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
4				0.213
9				0.024
2				0.001
1				0.0

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	29.13	0.894
2	3.15	0.086
3	2.42	0.053
4	1.59	0.021
5	1.47	0.017

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
5				0.61

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	11.67	0.62
2	1.32	0.015
3	1.22	0.011

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.

51 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
ADN	4XDR	O83774	267.2 Da LogP -1.98 TPSA 139.5	✓ Ro5	✓ Clean	`c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)…`

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
ZINC2047403	1.000	267.2 Da LogP -1.98 TPSA 139.5	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@H]1O[C@@H](CO)[C@@H](O)[C@@H]1O`
ZINC2047673	1.000	267.2 Da LogP -1.98 TPSA 139.5	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@@H](CO)[C@H](O)[C@@H]1O`
ZINC2169830	1.000	267.2 Da LogP -1.98 TPSA 139.5	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@H](CO)[C@@H](O)[C@H]1O`
ZINC3201876	1.000	267.2 Da LogP -1.98 TPSA 139.5	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@H]1O[C@H](CO)[C@@H](O)[C@@H]1O`
ZINC3201878	1.000	267.2 Da LogP -1.98 TPSA 139.5	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@@H](CO)[C@@H](O)[C@@H]…`
ZINC3830178	1.000	267.2 Da LogP -1.98 TPSA 139.5	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@H]1O[C@@H](CO)[C@@H](O)[C@H]1O`
ZINC3830179	1.000	267.2 Da LogP -1.98 TPSA 139.5	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@@H](CO)[C@@H](O)[C@H]1O`
ZINC3978047	1.000	267.2 Da LogP -1.98 TPSA 139.5	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@@H](CO)[C@H](O)[C@H]1O`
ZINC3978048	1.000	267.2 Da LogP -1.98 TPSA 139.5	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@H]1O[C@H](CO)[C@H](O)[C@H]1O`
ZINC3978049	1.000	267.2 Da LogP -1.98 TPSA 139.5	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@H](CO)[C@H](O)[C@H]1O`
ZINC4048240	1.000	267.2 Da LogP -1.98 TPSA 139.5	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@H]1O[C@H](CO)[C@@H](O)[C@H]1O`
ZINC8580514	1.000	267.2 Da LogP -1.98 TPSA 139.5	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@H](CO)[C@H](O)[C@@H]1O`
ZINC895113	1.000	267.2 Da LogP -1.98 TPSA 139.5	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@H]1O[C@@H](CO)[C@H](O)[C@@H]1O`
ZINC896706	1.000	267.2 Da LogP -1.98 TPSA 139.5	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@H]1O[C@@H](CO)[C@H](O)[C@H]1O`
ZINC970363	1.000	267.2 Da LogP -1.98 TPSA 139.5	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@H](CO)[C@@H](O)[C@@H]1O`
ZINC4188096	0.974	297.3 Da LogP -2.62 TPSA 159.8	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@H]1O[C@@H](CO)[C@@H](O)[C@@H](…`
ZINC4188103	0.974	297.3 Da LogP -2.62 TPSA 159.8	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@@H](CO)[C@@H](O)[C@@H]…`
ZINC4188112	0.974	297.3 Da LogP -2.62 TPSA 159.8	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@H]1O[C@@H](CO)[C@@H](O)[C@@H](…`
ZINC4188116	0.974	297.3 Da LogP -2.62 TPSA 159.8	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@@H](CO)[C@@H](O)[C@@H]…`
ZINC101227935	0.837	266.3 Da LogP -2.01 TPSA 145.3	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@H](CO)[C@H](O)[C@@H]1N`
ZINC1868288	0.837	266.3 Da LogP -2.01 TPSA 145.3	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@H](CO)[C@@H](O)[C@@H]1N`
ZINC39294072	0.837	266.3 Da LogP -2.01 TPSA 145.3	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@H](CO)[C@H](O)[C@H]1N`
ZINC53204366	0.837	266.3 Da LogP -2.01 TPSA 145.3	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@H](CO)[C@@H](O)[C@H]1N`
ZINC57675642	0.837	266.3 Da LogP -2.01 TPSA 145.3	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@H]1O[C@@H](CO)[C@@H](O)[C@H]1N`
ZINC57675644	0.837	266.3 Da LogP -2.01 TPSA 145.3	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@@H](CO)[C@@H](O)[C@H]1N`
ZINC57675648	0.837	266.3 Da LogP -2.01 TPSA 145.3	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@H]1O[C@@H](CO)[C@@H](O)[C@@H]1N`
ZINC57675649	0.837	266.3 Da LogP -2.01 TPSA 145.3	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@@H](CO)[C@@H](O)[C@@H]…`
ZINC71250611	0.837	266.3 Da LogP -2.01 TPSA 145.3	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@H]1O[C@@H](CO)[C@H](O)[C@@H]1N`
ZINC4809089	0.833	283.3 Da LogP -1.04 TPSA 119.3	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@H]1O[C@@H](CO)[C@@H](S)[C@H]1O`
ZINC4809090	0.833	283.3 Da LogP -1.04 TPSA 119.3	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@@H](CO)[C@@H](S)[C@H]1O`
ZINC4809091	0.833	283.3 Da LogP -1.04 TPSA 119.3	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@H]1O[C@@H](CO)[C@@H](S)[C@@H]1O`
ZINC4809092	0.833	283.3 Da LogP -1.04 TPSA 119.3	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@@H](CO)[C@@H](S)[C@@H]…`
ZINC5139067	0.829	283.3 Da LogP -1.04 TPSA 119.3	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@H](CS)[C@@H](O)[C@H]1O`
ZINC105358492	0.818	269.2 Da LogP -1.00 TPSA 119.3	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@H](CO)[C@H](O)[C@@H]1F`
ZINC22805	0.818	269.2 Da LogP -1.00 TPSA 119.3	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@H](CO)[C@@H](O)[C@@H]1F`
ZINC2383767290	0.818	269.2 Da LogP -1.00 TPSA 119.3	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@@H](CO)[C@H](O)[C@@H]1F`
ZINC3827883	0.818	269.2 Da LogP -1.00 TPSA 119.3	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@H]1O[C@@H](CO)[C@H](O)[C@H]1F`
ZINC5163038	0.818	269.2 Da LogP -1.00 TPSA 119.3	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@H](CO)[C@@H](O)[C@H]1F`
ZINC5372462	0.818	269.2 Da LogP -1.00 TPSA 119.3	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@@H](CO)[C@@H](O)[C@@H]…`
ZINC66155300	0.818	269.2 Da LogP -1.00 TPSA 119.3	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@H](CO)[C@H](O)[C@H]1F`
ZINC83323919	0.818	269.2 Da LogP -1.00 TPSA 119.3	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@H]1O[C@@H](CO)[C@H](O)[C@@H]1F`
ZINC13470207	0.814	266.3 Da LogP -2.01 TPSA 145.3	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@H](CO)[C@@H](N)[C@H]1O`
ZINC14418140	0.814	266.3 Da LogP -2.01 TPSA 145.3	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@H](CO)[C@H](N)[C@H]1O`
ZINC79682926	0.814	266.3 Da LogP -2.01 TPSA 145.3	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@H](CO)[C@H](N)[C@@H]1O`
ZINC3814316	0.810	266.3 Da LogP -2.01 TPSA 145.3	✓ Ro5	✓ Clean	`NC[C@H]1O[C@@H](n2cnc3c(N)ncnc32)[C@H](O)[C@@H]…`
ZINC4773848	0.810	266.3 Da LogP -2.01 TPSA 145.3	✓ Ro5	✓ Clean	`NC[C@@H]1O[C@H](n2cnc3c(N)ncnc32)[C@H](O)[C@@H]…`
ZINC4773849	0.810	266.3 Da LogP -2.01 TPSA 145.3	✓ Ro5	✓ Clean	`NC[C@@H]1O[C@@H](n2cnc3c(N)ncnc32)[C@H](O)[C@@H…`
ZINC4773850	0.810	266.3 Da LogP -2.01 TPSA 145.3	✓ Ro5	✓ Clean	`NC[C@@H]1O[C@H](n2cnc3c(N)ncnc32)[C@@H](O)[C@@H…`
ZINC4773851	0.810	266.3 Da LogP -2.01 TPSA 145.3	✓ Ro5	✓ Clean	`NC[C@@H]1O[C@@H](n2cnc3c(N)ncnc32)[C@@H](O)[C@@…`
ZINC77981211	0.810	266.3 Da LogP -2.01 TPSA 145.3	✓ Ro5	✓ Clean	`NC[C@H]1O[C@@H](n2cnc3c(N)ncnc32)[C@@H](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.