Protein profile

KP13_01935

Thiamine-binding periplasmic protein

Genome: KpKP13

Gene: thiB AHE46376.1 Structure source: AlphaFold + ColabFold UniProt A0A0H3GRM5

Export view

Amino acids 327

Annotations 3

Features 18

PDB binders 1

Druggability 0.928

Overview

Basic information about this protein and its source genome.

Accession: KP13_01935
Assembly: Klebsiella pneumoniae subsp. pneumoniae Kp13, complete sequence
Gene: thiB AHE46376.1
Status: annotated
Amino acids: 327
Structure source: AlphaFold + ColabFold

GO:0030975 Binding to thiamine (vitamin B1), a water soluble vitamin present in fresh vegetables and meats, especially liver. GO:0015888 The directed movement of thiamine into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. Thiamine is vitamin B1, a water soluble vitamin present in fresh vegetables and meats, especially liver. GO:0030288 The region between the inner (cytoplasmic or plasma) membrane and outer membrane of organisms with two membranes such as Gram negative bacteria. These periplasmic spaces are relatively thick and contain a thin peptidoglycan layer (PGL), also referred to as a thin cell wall.

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: Periplasmic
ColabFold pLDDT: 95.21

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 0.928

Structure A0A0H3GRM5

Pocket Pocket 1

P2Rank 0.778

Structure A0A0H3GRM5

Pocket Pocket 1

ColabFold model

FPocket 0.924 · Pocket 1

P2Rank 0.748 · Pocket 1

Core conservation Conserved core gene

Roary core

CoreCruncher core

Gut microbiome 135 / 4744 genomes with a hit

Normalized 0.028

Sequence

Primary amino-acid sequence viewer.

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

3 GO

Gene Ontology (GO)

GO:0030975 Binding to thiamine (vitamin B1), a water soluble vitamin present in fresh vegetables and meats, especially liver.
GO:0015888 The directed movement of thiamine into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. Thiamine is vitamin B1, a water soluble vitamin present in fresh vegetables and meats, especially liver.
GO:0030288 The region between the inner (cytoplasmic or plasma) membrane and outer membrane of organisms with two membranes such as Gram negative bacteria. These periplasmic spaces are relatively thick and contain a thin peptidoglycan layer (PGL), also referred to as a thin cell wall.

Sequence Features

Domain/signature hits from InterPro and related databases.

18 records

Show feature table

Start	End	DB	Term	Name
1	18	SignalP_GRAM_NEGATIVE	SignalP-noTM	SignalP-noTM
21	286	CDD	cd13545	PBP2_TbpA
21	286	InterPro	IPR005948	Thiamine/thiamin pyrophosphate-binding periplasmic protein, ABC transporter
123	322	Gene3D	G3DSA:3.40.190.10	-
9	327	PANTHER	PTHR30006	THIAMINE-BINDING PERIPLASMIC PROTEIN-RELATED
1	18	Phobius	SIGNAL_PEPTIDE	Signal peptide region
5	13	Phobius	SIGNAL_PEPTIDE_H_REGION	Hydrophobic region of a signal peptide.
1	18	SignalP_GRAM_POSITIVE	SignalP-TM	SignalP-TM
18	321	NCBIfam	TIGR01254	thiamine ABC transporter substrate-binding protein
18	321	InterPro	IPR005948	Thiamine/thiamin pyrophosphate-binding periplasmic protein, ABC transporter
19	327	Phobius	NON_CYTOPLASMIC_DOMAIN	Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
22	297	Gene3D	G3DSA:3.40.190.10	-
22	323	SUPERFAMILY	SSF53850	Periplasmic binding protein-like II
14	18	Phobius	SIGNAL_PEPTIDE_C_REGION	C-terminal region of a signal peptide.
8	327	NCBIfam	TIGR01276	thiamine ABC transporter substrate binding subunit
8	327	InterPro	IPR005967	Thiamin/thiamin pyrophosphate ABC transporter, substrate-binding protein, Proteobacteria
1	4	Phobius	SIGNAL_PEPTIDE_N_REGION	N-terminal region of a signal peptide.
73	290	Pfam	PF13343	Bacterial extracellular solute-binding protein

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_A0A0H3GRM5	AlphaFold	—	—	full sequence	—	Viewing
ColabFold KP13_01935	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
1				0.928

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	15.02	0.742
2	2.42	0.065
3	1.45	0.019

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				0.924

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	12.57	0.655
2	2.72	0.082
3	1.53	0.023

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.

25 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
TPS	2QRY	P31550	345.3 Da LogP 0.72 TPSA 122.4	✓ Ro5	✓ Clean	`Cc1c(sc[n+]1Cc2cnc(nc2N)C)CCOP(=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
ZINC1532839	1.000	345.3 Da LogP 0.72 TPSA 122.4	✓ Ro5	✓ Clean	`Cc1ncc(C[n+]2csc(CCOP(=O)(O)O)c2C)c(N)n1`
ZINC8215517	0.868	425.3 Da LogP 0.84 TPSA 169.0	✓ Ro5	✓ Clean	`Cc1ncc(C[n+]2csc(CCO[P@@](=O)(O)OP(=O)(O)O)c2C)…`
ZINC5159740	0.741	307.4 Da LogP 1.18 TPSA 82.0	✓ Ro5	✓ Clean	`CC(=O)OCCc1sc[n+](Cc2cnc(C)nc2N)c1C`
ZINC1569986051	0.722	324.5 Da LogP 1.50 TPSA 88.8	✓ Ro5	✓ Clean	`Cc1ncc(C[n+]2csc(CCOC(=N)S)c2C)c(N)n1`
ZINC65748831	0.714	345.4 Da LogP 0.43 TPSA 119.3	✓ Ro5	✓ Clean	`Cc1ncc(C[n+]2csc(CCOS(=O)(=O)O)c2C)c(N)n1`
ZINC13520374	0.707	426.3 Da LogP 0.97 TPSA 163.2	✓ Ro5	✓ Clean	`Cc1ncc(C[n+]2csc(CCO[P@@](=O)(O)OP(=O)(O)O)c2C)…`
ZINC49153	0.692	265.4 Da LogP 0.61 TPSA 75.9	✓ Ro5	✓ Clean	`Cc1ncc(C[n+]2csc(CCO)c2C)c(N)n1`
ZINC167956596	0.673	281.4 Da LogP 1.55 TPSA 55.7	✓ Ro5	✓ Clean	`Cc1ncc(C[n+]2csc(CCS)c2C)c(N)n1`
ZINC3209500	0.667	369.5 Da LogP 2.47 TPSA 82.0	✓ Ro5	✓ Clean	`Cc1ncc(C[n+]2csc(CCOC(=O)c3ccccc3)c2C)c(N)n1`
ZINC1497913	0.625	427.6 Da LogP 3.23 TPSA 82.0	✓ Ro5	✓ Clean	`Cc1ncc(C[n+]2csc(CCOC(=O)C3C4CC5CC(C4)CC3C5)c2C…`
ZINC8398853	0.625	441.6 Da LogP 3.77 TPSA 82.0	✓ Ro5	✓ Clean	`Cc1ncc(C[n+]2csc(CCOC(=O)CC34CC5CC(CC(C5)C3)C4)…`
ZINC1216218	0.606	387.5 Da LogP 2.74 TPSA 82.0	✓ Ro5	✓ Clean	`Cc1ncc(C[n+]2csc(CCOC(=O)C34CCC(CC3)C4)c2C)c(N)…`
ZINC101834499	0.597	387.5 Da LogP 2.59 TPSA 82.0	✓ Ro5	✓ Clean	`Cc1ncc(C[n+]2csc(CCOC(=O)[C@@H]3C[C@H]4CC[C@H]3…`
ZINC101834506	0.597	387.5 Da LogP 2.59 TPSA 82.0	✓ Ro5	✓ Clean	`Cc1ncc(C[n+]2csc(CCOC(=O)[C@H]3C[C@H]4CC[C@H]3C…`
ZINC100312511	0.571	441.6 Da LogP 3.77 TPSA 82.0	✓ Ro5	✓ Clean	`Cc1ncc(C[n+]2csc(CCOC(=O)C34C[C@H]5C[C@@H](CC(C…`
ZINC100471563	0.563	455.6 Da LogP 4.16 TPSA 82.0	✓ Ro5	✓ Clean	`Cc1ncc(C[n+]2csc(CCOC(=O)CC34C[C@H]5C[C@@H](CC(…`
ZINC1694013	0.559	281.4 Da LogP 0.31 TPSA 85.1	✓ Ro5	✓ Clean	`COc1ncc(C[n+]2csc(CCO)c2C)c(N)n1`
ZINC1694197	0.550	295.4 Da LogP 0.70 TPSA 85.1	✓ Ro5	✓ Clean	`CCOc1ncc(C[n+]2csc(CCO)c2C)c(N)n1`
ZINC1673584	0.542	279.4 Da LogP 0.86 TPSA 75.9	✓ Ro5	✓ Clean	`CCc1ncc(C[n+]2csc(CCO)c2C)c(N)n1`
ZINC1529994	0.538	219.1 Da LogP -0.02 TPSA 118.6	✓ Ro5	✓ Clean	`Cc1ncc(COP(=O)(O)O)c(N)n1`
ZINC231372391	0.536	264.4 Da LogP 1.33 TPSA 49.9	✓ Ro5	✓ Clean	`Cc1ncc(C[n+]2csc(CCO)c2C)c(C)n1`
ZINC59481311	0.517	279.3 Da LogP 1.42 TPSA 79.3	✓ Ro5	✓ Clean	`Cc1ncc(C[n+]2csc(CCO)c2C)c(N=O)n1`
ZINC13540298	0.507	440.3 Da LogP 0.72 TPSA 187.1	✓ Ro5	✓ Clean	`Cc1ncc(Cn2c(C)c(CCO[P@@](=O)(O)OP(=O)(O)O)sc2=O…`
ZINC13540412	0.500	251.3 Da LogP 0.30 TPSA 75.9	✓ Ro5	✓ Clean	`Cc1c(CCO)sc[n+]1Cc1cncnc1N`

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.