Protein profile

VK055_2849

methionine sulfoxide reductase A

Genome: KpATCC43816

Gene: msrA AIK81438.1 Structure source: AlphaFold + ColabFold UniProt A0A0H3GHE5

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Amino acids 212

Annotations 5

Features 12

PDB binders 6

Druggability 0.021

Overview

Basic information about this protein and its source genome.

Accession: VK055_2849
Assembly: Klebsiella pneumoniae subsp. pneumoniae strain ATCC 43816 KPPR1, complete genome
Gene: msrA AIK81438.1
Status: annotated
Amino acids: 212
Structure source: AlphaFold + ColabFold

1.8.4.11

GO:0008113 Catalysis of the reaction: L-methionyl-[protein] + [thioredoxin]-disulfide + H2O = L-methionyl-(S)-S-oxide-[protein] + [thioredoxin]-dithiol. GO:0005737 The contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures. GO:0033744 Catalysis of the reaction: [thioredoxin]-disulfide + L-methionine + H2O = L-methionine (S)-S-oxide + [thioredoxin]-dithiol. GO:0034599 Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of oxidative stress, a state often resulting from exposure to high levels of reactive oxygen species, e.g. superoxide anions, hydrogen peroxide (H2O2), and hydroxyl radicals.

Target profile

Computed evidence for target prioritization.

Human off-target: hit
Human identity (%): 70.732
Human E-value: 3.01e-41
Gut microbiome off-target: hit
Essential (DEG): N
DEG identity (%): 0.0
Localization: Unknown
ColabFold pLDDT: 95.54

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 0.021

Structure A0A0H3GHE5

Pocket Pocket 7

P2Rank 0.206

Structure A0A0H3GHE5

Pocket Pocket 1

ColabFold model

FPocket 0.378 · Pocket 6

P2Rank 0.204 · Pocket 1

Core conservation Conserved core gene

Roary core

CoreCruncher core

Gut microbiome 180 / 4744 genomes with a hit

Normalized 0.038

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)

1.8.4.11

Gene Ontology (GO)

GO:0008113 Catalysis of the reaction: L-methionyl-[protein] + [thioredoxin]-disulfide + H2O = L-methionyl-(S)-S-oxide-[protein] + [thioredoxin]-dithiol.
GO:0005737 The contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
GO:0033744 Catalysis of the reaction: [thioredoxin]-disulfide + L-methionine + H2O = L-methionine (S)-S-oxide + [thioredoxin]-dithiol.
GO:0034599 Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of oxidative stress, a state often resulting from exposure to high levels of reactive oxygen species, e.g. superoxide anions, hydrogen peroxide (H2O2), and hydroxyl radicals.

Sequence Features

Domain/signature hits from InterPro and related databases.

12 records

Show feature table

Start	End	DB	Term	Name
4	212	FunFam	G3DSA:3.30.1060.10:FF:000001	Peptide methionine sulfoxide reductase MsrA
46	199	Pfam	PF01625	Peptide methionine sulfoxide reductase
46	199	InterPro	IPR002569	Peptide methionine sulphoxide reductase MsrA domain
45	199	NCBIfam	TIGR00401	peptide-methionine (S)-S-oxide reductase MsrA
45	199	InterPro	IPR002569	Peptide methionine sulphoxide reductase MsrA domain
4	211	Gene3D	G3DSA:3.30.1060.10	Peptide methionine sulphoxide reductase MsrA
4	211	InterPro	IPR036509	Peptide methionine sulphoxide reductase MsrA superfamily
43	205	Hamap	MF_01401	Peptide methionine sulfoxide reductase MsrA [msrA].
43	205	InterPro	IPR002569	Peptide methionine sulphoxide reductase MsrA domain
37	200	PANTHER	PTHR42799	MITOCHONDRIAL PEPTIDE METHIONINE SULFOXIDE REDUCTASE
5	208	SUPERFAMILY	SSF55068	Peptide methionine sulfoxide reductase
5	208	InterPro	IPR036509	Peptide methionine sulphoxide reductase MsrA superfamily

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_A0A0H3GHE5	AlphaFold	—	—	full sequence	—	Viewing
ColabFold VK055_2849	ColabFold	—	—	full sequence	—	Loaded

Pocket details FPocket · P2Rank — toggle visibility and zoom from here, or open full viewer

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				4.11	0.166
2				1.12	0.008

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
6				0.378

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				3.63	0.136

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.

62 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
CAC	4D7L	Q6NEL2	137.0 Da LogP -0.52 TPSA 40.1	✓ Ro5	✓ Clean	`C[As](=O)(C)[O-]`
D1D	5FA9	Q73PT7	152.2 Da LogP 0.10 TPSA 40.5	✓ Ro5	✓ Clean	`C1[C@H]([C@@H](CSS1)O)O`
DTT	5FA9	Q73PT7	154.3 Da LogP -0.43 TPSA 40.5	✓ Ro5	✓ Clean	`C([C@@H]([C@H](CS)O)O)S`
MYR	2L90	Q9D6Y7	228.4 Da LogP 4.77 TPSA 37.3	✓ Ro5	✓ Clean	`CCCCCCCCCCCCCC(=O)O`
RSM	3HCH	Q9JWM8	220.3 Da LogP -0.99 TPSA 75.3	✓ Ro5	✓ Clean	`CC(=O)N[C@@H](CC[S@](=O)C)C(=O)NC`
SSM	3BQF	Q9JWM8	220.3 Da LogP -0.99 TPSA 75.3	✓ Ro5	✓ Clean	`CC(=O)N[C@@H](CC[S@@](=O)C)C(=O)NC`

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).

Ligand	UniProt (homolog)	pchembl	MW · LogP · TPSA	Lipinski	PAINS	SMILES
CHEMBL1350983	P54149	—	246.0 Da LogP -1.05 TPSA 94.8	✓ Ro5	✓ Clean	`O=C(O)c1ccccc1[As](=O)(O)O`
CHEMBL1445776	P54149	—	360.4 Da LogP 2.01 TPSA 77.3	✓ Ro5	Alert	`O=C1C(N2CCOCC2)=C(n2nnc3ccccc32)C(=O)c2ccccc21`
CHEMBL1563172	P54149	—	385.2 Da LogP 0.46 TPSA 154.3	✓ Ro5	Alert	`CSc1nc(N)c(N=Nc2ccc([As](=O)(O)O)cc2)c(O)n1`
CHEMBL1877709	P54149	—	438.5 Da LogP 3.82 TPSA 112.9	✓ Ro5	Alert	`O=C(O)c1ccc(NC2=C/C(=N/S(=O)(=O)c3cccs3)c3ccccc…`
CHEMBL1998302	P54149	—	432.5 Da LogP 3.76 TPSA 112.9	✓ Ro5	Alert	`O=C(O)c1ccc(NC2=C/C(=N/S(=O)(=O)c3ccccc3)c3cccc…`
CHEMBL3195410	P54149	—	460.5 Da LogP 4.32 TPSA 112.9	✓ Ro5	Alert	`CCc1ccc(S(=O)(=O)/N=C2\C=C(Nc3ccc(C(=O)O)cc3)C(…`

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
ZINC100432688	1.000	432.5 Da LogP 3.76 TPSA 112.9	✓ Ro5	Alert	`O=C(O)c1ccc(NC2=C/C(=N/S(=O)(=O)c3ccccc3)c3cccc…`
ZINC100610914	1.000	438.5 Da LogP 3.82 TPSA 112.9	✓ Ro5	Alert	`O=C(O)c1ccc(NC2=C/C(=N/S(=O)(=O)c3cccs3)c3ccccc…`
ZINC12501520	1.000	458.5 Da LogP -0.88 TPSA 123.5	1 viol.	✓ Clean	`OCCOCCOCCOCCOCCOCCOCCOCCOCCOCCO`
ZINC1282589	1.000	360.4 Da LogP 2.01 TPSA 77.3	✓ Ro5	Alert	`O=C1C(N2CCOCC2)=C(n2nnc3ccccc32)C(=O)c2ccccc21`
ZINC1529498	1.000	200.3 Da LogP 3.99 TPSA 37.3	✓ Ro5	✓ Clean	`CCCCCCCCCCCC(=O)O`
ZINC1530417	1.000	228.4 Da LogP 4.77 TPSA 37.3	✓ Ro5	✓ Clean	`CCCCCCCCCCCCCC(=O)O`
ZINC1628119	1.000	214.3 Da LogP 4.38 TPSA 37.3	✓ Ro5	✓ Clean	`CCCCCCCCCCCCC(=O)O`
ZINC3874716	1.000	414.5 Da LogP -0.90 TPSA 114.3	✓ Ro5	✓ Clean	`OCCOCCOCCOCCOCCOCCOCCOCCOCCO`
ZINC4283769	1.000	238.3 Da LogP -0.96 TPSA 77.4	✓ Ro5	✓ Clean	`OCCOCCOCCOCCOCCO`
ZINC4521548	1.000	282.3 Da LogP -0.95 TPSA 86.6	✓ Ro5	✓ Clean	`OCCOCCOCCOCCOCCOCCO`
ZINC5178829	1.000	326.4 Da LogP -0.93 TPSA 95.8	✓ Ro5	✓ Clean	`OCCOCCOCCOCCOCCOCCOCCO`
ZINC5178830	1.000	370.4 Da LogP -0.91 TPSA 105.1	✓ Ro5	✓ Clean	`OCCOCCOCCOCCOCCOCCOCCOCCO`
ZINC100822378	0.854	466.9 Da LogP 4.41 TPSA 112.9	✓ Ro5	Alert	`O=C(O)c1ccc(NC2=C/C(=N/S(=O)(=O)c3ccc(Cl)cc3)c3…`
ZINC102629392	0.854	450.4 Da LogP 3.89 TPSA 112.9	✓ Ro5	Alert	`O=C(O)c1ccc(NC2=C/C(=N/S(=O)(=O)c3ccc(F)cc3)c3c…`
ZINC102629400	0.854	446.5 Da LogP 4.06 TPSA 112.9	✓ Ro5	Alert	`Cc1ccc(S(=O)(=O)/N=C2/C=C(Nc3ccc(C(=O)O)cc3)C(=…`
ZINC138457918	0.850	228.3 Da LogP 3.56 TPSA 54.4	✓ Ro5	✓ Clean	`CCCCCCCC(=O)CCCCC(=O)O`
ZINC138458029	0.850	228.3 Da LogP 3.56 TPSA 54.4	✓ Ro5	✓ Clean	`CCCCCCC(=O)CCCCCC(=O)O`
ZINC144395054	0.850	242.4 Da LogP 3.95 TPSA 54.4	✓ Ro5	✓ Clean	`CCCCCC(=O)CCCCCCCC(=O)O`
ZINC14619628	0.850	270.4 Da LogP 4.73 TPSA 54.4	✓ Ro5	✓ Clean	`CCCCCC(=O)CCCCCCCCCC(=O)O`
ZINC196749828	0.850	214.3 Da LogP 3.17 TPSA 54.4	✓ Ro5	✓ Clean	`CCCCCCC(=O)CCCCC(=O)O`
ZINC2113934076	0.850	256.4 Da LogP 4.34 TPSA 54.4	✓ Ro5	✓ Clean	`CCCCCCC(=O)CCCCCCCC(=O)O`
ZINC2113934082	0.850	256.4 Da LogP 4.34 TPSA 54.4	✓ Ro5	✓ Clean	`CCCCCCCC(=O)CCCCCCC(=O)O`
ZINC2113934083	0.850	256.4 Da LogP 4.34 TPSA 54.4	✓ Ro5	✓ Clean	`CCCCCCCCCC(=O)CCCCC(=O)O`
ZINC2243670	0.850	228.3 Da LogP 3.56 TPSA 54.4	✓ Ro5	✓ Clean	`CCCCCC(=O)CCCCCCC(=O)O`
ZINC2569203	0.850	214.3 Da LogP 3.17 TPSA 54.4	✓ Ro5	✓ Clean	`CCCCCC(=O)CCCCCC(=O)O`
ZINC4798470	0.850	270.4 Da LogP 4.73 TPSA 54.4	✓ Ro5	✓ Clean	`CCCCCCC(=O)CCCCCCCCC(=O)O`
ZINC5973005	0.850	242.4 Da LogP 3.95 TPSA 54.4	✓ Ro5	✓ Clean	`CCCCCCC(=O)CCCCCCC(=O)O`
ZINC71418182	0.850	270.4 Da LogP 4.73 TPSA 54.4	✓ Ro5	✓ Clean	`CCCCCCCCCCC(=O)CCCCC(=O)O`
ZINC79244776	0.850	270.4 Da LogP 4.73 TPSA 54.4	✓ Ro5	✓ Clean	`CCCCCCCC(=O)CCCCCCCC(=O)O`
ZINC86037082	0.850	270.4 Da LogP 4.73 TPSA 54.4	✓ Ro5	✓ Clean	`CCCCCCCCCC(=O)CCCCCC(=O)O`
ZINC86037089	0.850	270.4 Da LogP 4.73 TPSA 54.4	✓ Ro5	✓ Clean	`CCCCCCCCC(=O)CCCCCCC(=O)O`
ZINC86039283	0.850	242.4 Da LogP 3.95 TPSA 54.4	✓ Ro5	✓ Clean	`CCCCCCCCC(=O)CCCCC(=O)O`
ZINC100919209	0.837	490.5 Da LogP 3.54 TPSA 139.2	✓ Ro5	Alert	`COC(=O)c1ccc(NC2=C/C(=N/S(=O)(=O)c3ccc(C(=O)O)c…`
ZINC100822310	0.830	452.5 Da LogP 3.91 TPSA 101.9	✓ Ro5	Alert	`COC(=O)c1ccc(NC2=C/C(=N/S(=O)(=O)c3cccs3)c3cccc…`
ZINC100822381	0.820	460.5 Da LogP 4.32 TPSA 112.9	✓ Ro5	Alert	`CCc1ccc(S(=O)(=O)/N=C2/C=C(Nc3ccc(C(=O)O)cc3)C(…`
ZINC102919871	0.820	474.5 Da LogP 4.88 TPSA 112.9	✓ Ro5	Alert	`CC(C)c1ccc(S(=O)(=O)/N=C2/C=C(Nc3ccc(C(=O)O)cc3…`
ZINC16873016	0.820	460.5 Da LogP 4.32 TPSA 112.9	✓ Ro5	Alert	`CCc1ccc(S(=O)(=O)N=C2C=C(Nc3ccc(C(=O)O)cc3)C(=O…`
ZINC3160730	0.810	214.3 Da LogP 3.17 TPSA 54.4	✓ Ro5	✓ Clean	`CCCCCCCC(=O)CCCC(=O)O`
ZINC4582907	0.810	200.3 Da LogP 2.78 TPSA 54.4	✓ Ro5	✓ Clean	`CCCCCCC(=O)CCCC(=O)O`
ZINC4727003	0.810	312.4 Da LogP 4.69 TPSA 71.4	✓ Ro5	✓ Clean	`CCCCCCC(=O)CCC(=O)CCCCCCCC(=O)O`
ZINC86037074	0.810	270.4 Da LogP 4.73 TPSA 54.4	✓ Ro5	✓ Clean	`CCCCCCCCCCCC(=O)CCCC(=O)O`
ZINC102205938	0.804	462.5 Da LogP 3.76 TPSA 122.1	✓ Ro5	Alert	`COc1ccc(S(=O)(=O)/N=C2/C=C(Nc3ccc(C(=O)O)cc3)C(…`
ZINC100822394	0.800	438.5 Da LogP 3.82 TPSA 112.9	✓ Ro5	Alert	`O=C(O)c1cccc(NC2=C/C(=N/S(=O)(=O)c3cccs3)c3cccc…`
ZINC2378801	0.800	200.3 Da LogP 2.78 TPSA 54.4	✓ Ro5	✓ Clean	`CCCCCC(=O)CCCCC(=O)O`
ZINC100478511	0.788	410.5 Da LogP 3.82 TPSA 95.8	✓ Ro5	Alert	`O=C1C(Nc2ccc(O)cc2)=C/C(=N/S(=O)(=O)c2cccs2)c2c…`
ZINC103721003	0.784	482.5 Da LogP 4.91 TPSA 112.9	✓ Ro5	Alert	`O=C(O)c1ccc(NC2=C/C(=N/S(=O)(=O)c3ccc4ccccc4c3)…`
ZINC102930303	0.783	404.4 Da LogP 3.76 TPSA 95.8	✓ Ro5	Alert	`O=C1C(Nc2ccc(O)cc2)=C/C(=N/S(=O)(=O)c2ccccc2)c2…`
ZINC102920855	0.776	432.5 Da LogP 3.76 TPSA 112.9	✓ Ro5	Alert	`O=C(O)c1cccc(NC2=C/C(=N/S(=O)(=O)c3ccccc3)c3ccc…`
ZINC2697774	0.773	435.5 Da LogP 3.50 TPSA 71.3	✓ Ro5	Alert	`O=C1C(N2CCN(c3ccccc3)CC2)=C(n2nnc3ccccc32)C(=O)…`
ZINC100919212	0.769	460.5 Da LogP 4.37 TPSA 112.9	✓ Ro5	Alert	`Cc1ccc(NC2=C/C(=N/S(=O)(=O)c3ccc(C(=O)O)cc3)c3c…`

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.