Protein profile

KP13_31609

Thiamine-phosphate synthase

Genome: KpKP13

Gene: AHE46928.1 thiE Structure source: AlphaFold + ColabFold UniProt A0A0H3GGQ3

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Amino acids 211

Annotations 6

Features 14

PDB binders 10

Druggability 0.713

Overview

Basic information about this protein and its source genome.

Accession: KP13_31609
Assembly: Klebsiella pneumoniae subsp. pneumoniae Kp13, complete sequence
Gene: AHE46928.1 thiE
Status: annotated
Amino acids: 211
Structure source: AlphaFold + ColabFold

2.5.1.3

GO:0009228 The chemical reactions and pathways resulting in the formation of thiamine (vitamin B1), a water soluble vitamin present in fresh vegetables and meats, especially liver. GO:0004789 Catalysis of the reaction: 4-amino-2-methyl-5-diphosphomethylpyrimidine + 4-methyl-5-(2-phosphoethyl)-thiazole + H+ = diphosphate + thiamine phosphate. GO:0005737 The contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures. GO:0000287 Binding to a magnesium (Mg) ion. GO:0009229 The chemical reactions and pathways resulting in the formation of thiamine diphosphate, a derivative of thiamine (vitamin B1) which acts as a coenzyme in a range of processes including the Krebs cycle.

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 (%): 57.368
DEG E-value: 6.68e-62
Localization: Cytoplasmic
ColabFold pLDDT: 95.22

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 0.713

Structure A0A0H3GGQ3

Pocket Pocket 1

P2Rank 0.943

Structure A0A0H3GGQ3

Pocket Pocket 1

ColabFold model

FPocket 0.547 · Pocket 3

P2Rank 0.94 · Pocket 1

Core conservation Conserved core gene

Roary core

CoreCruncher core

Gut microbiome 145 / 4744 genomes with a hit

Normalized 0.031

Sequence

Primary amino-acid sequence viewer.

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 5 GO

Enzyme Commission (EC)

2.5.1.3

Gene Ontology (GO)

GO:0009228 The chemical reactions and pathways resulting in the formation of thiamine (vitamin B1), a water soluble vitamin present in fresh vegetables and meats, especially liver.
GO:0004789 Catalysis of the reaction: 4-amino-2-methyl-5-diphosphomethylpyrimidine + 4-methyl-5-(2-phosphoethyl)-thiazole + H+ = diphosphate + thiamine phosphate.
GO:0005737 The contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
GO:0000287 Binding to a magnesium (Mg) ion.
GO:0009229 The chemical reactions and pathways resulting in the formation of thiamine diphosphate, a derivative of thiamine (vitamin B1) which acts as a coenzyme in a range of processes including the Krebs cycle.

Sequence Features

Domain/signature hits from InterPro and related databases.

14 records

Show feature table

Start	End	DB	Term	Name
8	206	FunFam	G3DSA:3.20.20.70:FF:000064	Thiamine-phosphate synthase
20	202	NCBIfam	TIGR00693	thiamine phosphate synthase
20	202	InterPro	IPR034291	Thiamine phosphate synthase
15	203	CDD	cd00564	TMP_TenI
15	203	InterPro	IPR022998	Thiamine phosphate synthase/TenI
10	207	Hamap	MF_00097	Thiamine-phosphate synthase [thiE].
10	207	InterPro	IPR034291	Thiamine phosphate synthase
9	205	Gene3D	G3DSA:3.20.20.70	Aldolase class I
9	205	InterPro	IPR013785	Aldolase-type TIM barrel
6	204	SUPERFAMILY	SSF51391	Thiamin phosphate synthase
6	204	InterPro	IPR036206	Thiamin phosphate synthase superfamily
13	205	PANTHER	PTHR20857	THIAMINE-PHOSPHATE PYROPHOSPHORYLASE
21	189	Pfam	PF02581	Thiamine monophosphate synthase
21	189	InterPro	IPR022998	Thiamine phosphate synthase/TenI

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_A0A0H3GGQ3	AlphaFold	—	—	full sequence	—	Viewing
ColabFold KP13_31609	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				0.713

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				22.49	0.881

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
3				0.547
1				0.49

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				20.9	0.863

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.

60 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
3NM	3O15	P39594	267.2 Da LogP 0.80 TPSA 117.0	✓ Ro5	✓ Clean	`Cc1c(sc(n1)C(=O)O)CCOP(=O)(O)O`
ACP	3NL5	Q6FV03	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)…`
FQP	1G4P	P39594	353.1 Da LogP 0.80 TPSA 165.1	✓ Ro5	✓ Clean	`c1c(c(nc(n1)C(F)(F)F)N)CO[P@](=O)(O)OP(=O)(O)O`
FTP	1G4T	P39594	397.3 Da LogP 0.17 TPSA 128.1	✓ Ro5	✓ Clean	`Cc1c(sc[n+]1Cc2cnc(nc2N)C(F)(F)F)CCOP(=O)([O-])…`
ICP	1G67	P39594	121.1 Da LogP 1.02 TPSA 48.6	✓ Ro5	✓ Clean	`CC1=NC(=N)C(=C)C=N1`
IFP	1G6C	P39594	175.1 Da LogP 1.57 TPSA 48.6	✓ Ro5	✓ Clean	`C=C1C=NC(=NC1=N)C(F)(F)F`
POP	1G4S	P39594	176.0 Da LogP -2.08 TPSA 129.9	✓ Ro5	✓ Clean	`O[P@@](=O)([O-])O[P@@](=O)(O)[O-]`
TPS	1G4S	P39594	345.3 Da LogP 0.72 TPSA 122.4	✓ Ro5	✓ Clean	`Cc1c(sc[n+]1Cc2cnc(nc2N)C)CCOP(=O)(O)O`
TZE	3NL5	Q6FV03	143.2 Da LogP 0.99 TPSA 33.1	✓ Ro5	✓ Clean	`Cc1c(scn1)CCO`
TZP	1G67	P39594	223.2 Da LogP 1.10 TPSA 79.7	✓ Ro5	✓ Clean	`Cc1c(scn1)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`
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)…`
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)…`
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…`
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)…`
ZINC1772820626	0.784	303.2 Da LogP 1.22 TPSA 126.2	✓ Ro5	✓ Clean	`Cc1ncsc1CCO[P@](=O)(O)OP(=O)(O)O`
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…`
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…`
ZINC5159740	0.741	307.4 Da LogP 1.18 TPSA 82.0	✓ Ro5	✓ Clean	`CC(=O)OCCc1sc[n+](Cc2cnc(C)nc2N)c1C`
ZINC105372833	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…`
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](…`
ZINC31475423	0.726	434.3 Da LogP -2.99 TPSA 238.4	2 viol.	✓ Clean	`Nc1ncnc2c1ncn2[C@H]1O[C@H](CO[P@@](=O)(O)OC(=O)…`
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)…`
ZINC5615251	0.700	375.3 Da LogP -0.55 TPSA 164.1	1 viol.	✓ Clean	`COP(=O)(OC)OC[C@H]1O[C@@H](n2cnc3c(N)ncnc32)[C@…`
ZINC5615253	0.700	375.3 Da LogP -0.55 TPSA 164.1	1 viol.	✓ Clean	`COP(=O)(OC)OC[C@@H]1O[C@@H](n2cnc3c(N)ncnc32)[C…`
ZINC5615258	0.700	375.3 Da LogP -0.55 TPSA 164.1	1 viol.	✓ Clean	`COP(=O)(OC)OC[C@H]1O[C@@H](n2cnc3c(N)ncnc32)[C@…`
ZINC5615263	0.700	375.3 Da LogP -0.55 TPSA 164.1	1 viol.	✓ Clean	`COP(=O)(OC)OC[C@@H]1O[C@@H](n2cnc3c(N)ncnc32)[C…`
ZINC31516918	0.692	446.4 Da LogP -1.33 TPSA 218.2	1 viol.	✓ Clean	`CC(C)[C@H](N)C(=O)O[P@](=O)(O)OC[C@H]1O[C@@H](n…`
ZINC49153	0.692	265.4 Da LogP 0.61 TPSA 75.9	✓ Ro5	✓ Clean	`Cc1ncc(C[n+]2csc(CCO)c2C)c(N)n1`
ZINC1582675	0.689	403.3 Da LogP 0.23 TPSA 164.1	1 viol.	✓ Clean	`CCOP(=O)(OCC)OC[C@H]1O[C@@H](n2cnc3c(N)ncnc32)[…`
ZINC5486730	0.689	403.3 Da LogP 0.23 TPSA 164.1	1 viol.	✓ Clean	`CCOP(=O)(OCC)OC[C@H]1O[C@@H](n2cnc3c(N)ncnc32)[…`
ZINC5486734	0.689	403.3 Da LogP 0.23 TPSA 164.1	1 viol.	✓ Clean	`CCOP(=O)(OCC)OC[C@@H]1O[C@@H](n2cnc3c(N)ncnc32)…`
ZINC5486740	0.689	403.3 Da LogP 0.23 TPSA 164.1	1 viol.	✓ Clean	`CCOP(=O)(OCC)OC[C@@H]1O[C@@H](n2cnc3c(N)ncnc32)…`
ZINC167956596	0.673	281.4 Da LogP 1.55 TPSA 55.7	✓ Ro5	✓ Clean	`Cc1ncc(C[n+]2csc(CCS)c2C)c(N)n1`
ZINC34718739	0.672	444.3 Da LogP -1.04 TPSA 206.6	2 viol.	✓ Clean	`O=P(O)(O)O[P@](=O)(O)OC[C@@H]1O[C@@H](n2cnc3c(S…`
ZINC34718740	0.672	444.3 Da LogP -1.04 TPSA 206.6	2 viol.	✓ Clean	`O=P(O)(O)O[P@](=O)(O)OC[C@@H]1O[C@H](n2cnc3c(S)…`

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.