Protein profile

VK055_0424

NMT1/THI5 like family protein

Genome: KpATCC43816

Gene: AIK79050.1 Structure source: AlphaFold + ColabFold UniProt A0A0H3GP99

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Amino acids 327

Annotations 1

Features 15

PDB binders 1

Druggability 0.3

Overview

Basic information about this protein and its source genome.

Accession: VK055_0424
Assembly: Klebsiella pneumoniae subsp. pneumoniae strain ATCC 43816 KPPR1, complete genome
Gene: AIK79050.1
Status: annotated
Amino acids: 327
Structure source: AlphaFold + ColabFold

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.

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 (%): 41.096
DEG E-value: 1.05e-66
Localization: Unknown
ColabFold pLDDT: 93.06

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 0.3

Structure A0A0H3GP99

Pocket Pocket 13

P2Rank 0.92

Structure A0A0H3GP99

Pocket Pocket 1

ColabFold model

FPocket 0.409 · Pocket 10

P2Rank 0.943 · Pocket 1

Core conservation Accessory gene

Roary accessory

CoreCruncher accessory

Gut microbiome 7 / 4744 genomes with a hit

Normalized 0.001

Sequence

Primary amino-acid sequence viewer.

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 GO

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.

Sequence Features

Domain/signature hits from InterPro and related databases.

15 records

Show feature table

Start	End	DB	Term	Name
5	321	PANTHER	PTHR31528	4-AMINO-5-HYDROXYMETHYL-2-METHYLPYRIMIDINE PHOSPHATE SYNTHASE THI11-RELATED
5	321	InterPro	IPR027939	NMT1/THI5 family
1	25	Phobius	SIGNAL_PEPTIDE	Signal peptide region
110	205	Gene3D	G3DSA:3.40.190.10	-
1	23	ProSiteProfiles	PS51257	Prokaryotic membrane lipoprotein lipid attachment site profile.
1	25	SignalP_GRAM_NEGATIVE	SignalP-noTM	SignalP-noTM
1	25	SignalP_GRAM_POSITIVE	SignalP-TM	SignalP-TM
26	327	Phobius	NON_CYTOPLASMIC_DOMAIN	Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
1	4	Phobius	SIGNAL_PEPTIDE_N_REGION	N-terminal region of a signal peptide.
39	242	Pfam	PF09084	NMT1/THI5 like
39	242	InterPro	IPR015168	SsuA/THI5-like
5	17	Phobius	SIGNAL_PEPTIDE_H_REGION	Hydrophobic region of a signal peptide.
31	298	Gene3D	G3DSA:3.40.190.10	-
30	242	SUPERFAMILY	SSF53850	Periplasmic binding protein-like II
18	25	Phobius	SIGNAL_PEPTIDE_C_REGION	C-terminal region of a signal peptide.

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_A0A0H3GP99	AlphaFold	—	—	full sequence	—	Viewing
ColabFold VK055_0424	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
13				0.3
2				0.005
9				0.001

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				33.13	0.92
2				1.2	0.009

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
10				0.409
13				0.013
8				0.001

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				38.77	0.943
2				1.0	0.005

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.

30 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
VIB	4NMY	Q187U0	265.4 Da LogP 0.61 TPSA 75.9	✓ Ro5	✓ Clean	`Cc1c(sc[n+]1Cc2cnc(nc2N)C)CCO`

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
ZINC49153	1.000	265.4 Da LogP 0.61 TPSA 75.9	✓ Ro5	✓ Clean	`Cc1ncc(C[n+]2csc(CCO)c2C)c(N)n1`
ZINC167956596	0.795	281.4 Da LogP 1.55 TPSA 55.7	✓ Ro5	✓ Clean	`Cc1ncc(C[n+]2csc(CCS)c2C)c(N)n1`
ZINC231372391	0.773	264.4 Da LogP 1.33 TPSA 49.9	✓ Ro5	✓ Clean	`Cc1ncc(C[n+]2csc(CCO)c2C)c(C)n1`
ZINC1673584	0.766	279.4 Da LogP 0.86 TPSA 75.9	✓ Ro5	✓ Clean	`CCc1ncc(C[n+]2csc(CCO)c2C)c(N)n1`
ZINC1694013	0.750	281.4 Da LogP 0.31 TPSA 85.1	✓ Ro5	✓ Clean	`COc1ncc(C[n+]2csc(CCO)c2C)c(N)n1`
ZINC1569986051	0.735	324.5 Da LogP 1.50 TPSA 88.8	✓ Ro5	✓ Clean	`Cc1ncc(C[n+]2csc(CCOC(=N)S)c2C)c(N)n1`
ZINC1694197	0.735	295.4 Da LogP 0.70 TPSA 85.1	✓ Ro5	✓ Clean	`CCOc1ncc(C[n+]2csc(CCO)c2C)c(N)n1`
ZINC5159740	0.720	307.4 Da LogP 1.18 TPSA 82.0	✓ Ro5	✓ Clean	`CC(=O)OCCc1sc[n+](Cc2cnc(C)nc2N)c1C`
ZINC13540412	0.717	251.3 Da LogP 0.30 TPSA 75.9	✓ Ro5	✓ Clean	`Cc1c(CCO)sc[n+]1Cc1cncnc1N`
ZINC59481311	0.694	279.3 Da LogP 1.42 TPSA 79.3	✓ Ro5	✓ Clean	`Cc1ncc(C[n+]2csc(CCO)c2C)c(N=O)n1`
ZINC1532839	0.692	345.3 Da LogP 0.72 TPSA 122.4	✓ Ro5	✓ Clean	`Cc1ncc(C[n+]2csc(CCOP(=O)(O)O)c2C)c(N)n1`
ZINC65748831	0.692	345.4 Da LogP 0.43 TPSA 119.3	✓ Ro5	✓ Clean	`Cc1ncc(C[n+]2csc(CCOS(=O)(=O)O)c2C)c(N)n1`
ZINC13983227	0.681	264.4 Da LogP 1.21 TPSA 63.0	✓ Ro5	✓ Clean	`Cc1ccc(C[n+]2csc(CCO)c2C)c(N)n1`
ZINC8215517	0.655	425.3 Da LogP 0.84 TPSA 169.0	✓ Ro5	✓ Clean	`Cc1ncc(C[n+]2csc(CCO[P@@](=O)(O)OP(=O)(O)O)c2C)…`
ZINC3209500	0.643	369.5 Da LogP 2.47 TPSA 82.0	✓ Ro5	✓ Clean	`Cc1ncc(C[n+]2csc(CCOC(=O)c3ccccc3)c2C)c(N)n1`
ZINC95630521	0.633	251.3 Da LogP 0.30 TPSA 75.9	✓ Ro5	✓ Clean	`Cc1ncc(C[n+]2csc(CCO)c2)c(N)n1`
ZINC1497913	0.600	427.6 Da LogP 3.23 TPSA 82.0	✓ Ro5	✓ Clean	`Cc1ncc(C[n+]2csc(CCOC(=O)C3C4CC5CC(C4)CC3C5)c2C…`
ZINC8398853	0.600	441.6 Da LogP 3.77 TPSA 82.0	✓ Ro5	✓ Clean	`Cc1ncc(C[n+]2csc(CCOC(=O)CC34CC5CC(CC(C5)C3)C4)…`
ZINC902189	0.600	259.3 Da LogP 0.55 TPSA 75.9	✓ Ro5	✓ Clean	`Cc1ncc(C[n+]2cccc(CCO)c2C)c(N)n1`
ZINC13520371	0.588	266.3 Da LogP 0.32 TPSA 69.9	✓ Ro5	✓ Clean	`Cc1ncc(C[n+]2csc(CCO)c2C)c(=O)[nH]1`
ZINC1216218	0.581	387.5 Da LogP 2.74 TPSA 82.0	✓ Ro5	✓ Clean	`Cc1ncc(C[n+]2csc(CCOC(=O)C34CCC(CC3)C4)c2C)c(N)…`
ZINC15449131	0.580	265.4 Da LogP 0.61 TPSA 75.9	✓ Ro5	✓ Clean	`Cc1nc(N)cc(C[n+]2csc(CCO)c2C)n1`
ZINC101834499	0.571	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	0.571	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…`
ZINC313232	0.549	257.3 Da LogP 1.92 TPSA 55.7	✓ Ro5	✓ Clean	`Cc1ncc(C[n+]2csc3ccccc32)c(N)n1`
ZINC100312511	0.545	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	0.537	455.6 Da LogP 4.16 TPSA 82.0	✓ Ro5	✓ Clean	`Cc1ncc(C[n+]2csc(CCOC(=O)CC34C[C@H]5C[C@@H](CC(…`
ZINC13520374	0.517	426.3 Da LogP 0.97 TPSA 163.2	✓ Ro5	✓ Clean	`Cc1ncc(C[n+]2csc(CCO[P@@](=O)(O)OP(=O)(O)O)c2C)…`
ZINC4110282	0.500	234.3 Da LogP 1.93 TPSA 24.1	✓ Ro5	✓ Clean	`Cc1c(CCO)sc[n+]1Cc1ccccc1`

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.