Protein target profile

VK055_2849

methionine sulfoxide reductase A

Genome: KpATCC43816 Gene: msrA AIK81438.1 3D evidence: AlphaFold DB model + ColabFold model UniProt A0A0H3GHE5

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Length 212

Pocket druggability 0.021

Direct ligand evidence 0 62 total records

Functional annotation 1 EC 4 GO

Target summary

Target candidate with partial support; inspect missing evidence before prioritizing.

Automated synthesis of the evidence currently loaded. Review the underlying records before prioritizing this protein.

Terms and data sources used on this page

PDB: experimentally determined structures from the Protein Data Bank. These are the strongest structural evidence, but may cover only part of the protein.

AlphaFold DB model: a precomputed predicted structure downloaded from AlphaFold Database/UniProt, not an experiment performed here.

ColabFold model: a predicted structure generated for this workspace; interpret it with coverage and confidence.

pLDDT: confidence score for predicted structures. High values support local geometry; low values mean the region should not drive pocket interpretation.

FPocket / P2Rank: software tools that predict possible ligand-binding pockets on a 3D structure. They are useful screening signals, not experimental validation.

Druggability: a pocket-based estimate of whether a small molecule could bind productively. It does not mean a drug already exists.

PDB ligand: a compound observed in an experimental structure. Direct same-protein records are stronger than homolog-transferred records.

ChEMBL: a public database of measured compound bioactivity. Direct entries are stronger than entries transferred from similar proteins.

ZINC: a purchasable-compound database. Here it marks proposed candidates from chemical similarity, not measured binders.

LigQ / LigQ_2: an internal Target pipeline step that gathers PDB, ChEMBL, and ZINC ligand evidence for each protein.

Off-target: sequence similarity to proteins we prefer not to hit, such as human proteins or beneficial gut microbiome proteins.

DEG: Database of Essential Genes. A match suggests the protein resembles genes known to be essential in other organisms.

Roary / CoreCruncher: pan-genome tools used to decide whether a gene is core across analyzed strains or accessory/strain-specific.

EC / GO: functional annotations: EC describes enzyme reactions; GO describes biological process, molecular function, or cellular component.

KEGG pathway: a curated metabolic route label used here to group reactions imported from the metabolic model.

Chokepoint: a metabolic reaction that is the only producer or consumer of a metabolite in the imported model.

Prioritization evidence

Selectivity, essentiality, structural confidence, conservation, and predicted binding-site evidence.

Off-target risk

Human off-target: Hit
Human identity (%): 70.732 Lower values reduce human off-target concern.
Human E-value: 3.01e-41
Gut microbiome similarity: 3.8% of screened genomes Lower prevalence suggests narrower overlap with the screened gut microbiome.

Essentiality

Essential (DEG): N
DEG identity (%): 0.0 Higher values support similarity to known essential genes.

Localization

Localization: Unknown

Structure confidence

ColabFold pLDDT: 95.54 0-100 confidence; >70 supports local structural interpretation.

Binding-site evidence

AlphaFold DB / UniProt model

The selected pocket score is the FPocket value used for ranking after applying the curated structure priority. It estimates small-molecule pocket quality; it is not experimental binding evidence. The 3D viewer may show a different loaded structure, so 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

Prevalence 3.8%

Cross-references

External database identifiers for this protein, its structures, ligands, and metabolic reactions.

Sequence

UniProt A0A0H3GHE5

Chemistry

ChEMBL CHEMBL1350983 ChEMBL CHEMBL1445776 ChEMBL CHEMBL1563172 ChEMBL CHEMBL1877709 ChEMBL CHEMBL1998302 ChEMBL CHEMBL3195410

Sequence

Primary amino-acid sequence viewer.

MSLFDKTHLVAQADALPGRNTPMPVATLHAVNGHSMTNVPAGMEVALFAMGCFWGVERLFWQLPGVYSTAAGYTGGYTPNPTYREVCSGQTGHAEAVRVVYDPQVISYEQLLQVFWENHDPAQGMRQGNDHGTQYRSAIYPLTPEQTEAAKASLARFQAAMNDAHDTRHITTEIATAKPFYYAEDDHQQYLYKNPHGYCGIGGIGVCLPPQA

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 domains and features

Domain and signature matches imported 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; AlphaFold DB and ColabFold models typically cover the full protein but remain computational predictions.

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Pocket score High Medium Low

How colors and pocket overlays are used

Uniform protein color marks the displayed model as a single molecular object.

Experimental PDB structures may be colored by chain to distinguish subunits or copies present in the file.

Pocket colors and alpha spheres are evidence overlays for predicted binding cavities; they are not alternative protein chains.

'Alpha spheres' is FPocket's own cavity-shape geometry, imported when available and aligned with the loaded structure.

'Pocket atoms'/'Predicted site atoms' show the pocket's residue atoms instead: P2Rank reports residues rather than alpha spheres, and FPocket falls back to this when alpha-sphere geometry is unavailable or doesn't align.

'No pocket geometry' means neither alpha spheres nor residue-position data could be found for that pocket; the layer just highlights the same residues as 'Nearby residues'.

Pocket details Inspect a specific pocket, or open the full viewer

Binding pockets · P2Rank

Probability: high ≥ 0.5 · medium 0.2–0.49 · low < 0.2

Site 1 P2Rank #1

0.206

Show in viewer

Surrounding area

Site 2 P2Rank #2

0.011

Show in viewer

Surrounding area

Residue sets

UniProt: Active site:52-52

All structural evidence 0 experimental · 2 predicted

Structural evidence

0 + 2

Experimental PDB entries plus predicted AlphaFold DB or ColabFold models. Click Switch to display a different loaded structure in the viewer.

Entry	Method	Resolution	Chain	Coverage	Links	Status
AlphaFold DB AF_A0A0H3GHE5	AlphaFold DB	—	—	full sequence	—	Viewing
ColabFold VK055_2849	ColabFold	—	—	full sequence	—	Loaded

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

Chemistry signal

Structural and bioactivity evidence are both available for this target.

Direct evidence 0 same-protein records

Transferred evidence 12 records from similar proteins

Structural ligands 6 0 loaded crystals

Measured bioactivity 6 direct and transferred ChEMBL records

Proposed compounds 50 similarity-based ZINC candidates

Best available ligand signal

CAC PDB via homolog 137.0 Da · LogP -0.52 · TPSA 40.1 Open detail RCSB PDB

D1D PDB via homolog Detail RCSB PDB

DTT PDB via homolog Detail RCSB PDB

MYR PDB via homolog Detail RCSB PDB

RSM PDB via homolog Detail RCSB PDB

Highest-confidence structural evidence: ligands co-crystallized with this exact protein. If the source PDB is loaded in Target, 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 RCSB PDB	4D7L	Q6NEL2	137.0 Da LogP -0.52 TPSA 40.1	✓ Ro5	✓ Clean	`C[As](=O)(C)[O-]`
D1D RCSB PDB	5FA9	Q73PT7	152.2 Da LogP 0.10 TPSA 40.5	✓ Ro5	✓ Clean	`C1[C@H]([C@@H](CSS1)O)O`
DTT RCSB PDB	5FA9	Q73PT7	154.3 Da LogP -0.43 TPSA 40.5	✓ Ro5	✓ Clean	`C([C@@H]([C@H](CS)O)O)S`
MYR RCSB PDB	2L90	Q9D6Y7	228.4 Da LogP 4.77 TPSA 37.3	✓ Ro5	✓ Clean	`CCCCCCCCCCCCCC(=O)O`
RSM RCSB PDB	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 RCSB PDB	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 ChEMBL	P54149	—	246.0 Da LogP -1.05 TPSA 94.8	✓ Ro5	✓ Clean	`O=C(O)c1ccccc1[As](=O)(O)O`
CHEMBL1445776 ChEMBL	P54149	—	360.4 Da LogP 2.01 TPSA 77.3	✓ Ro5	Alert	`O=C1C(N2CCOCC2)=C(n2nnc3ccccc32)C(=O)c2ccccc21`
CHEMBL1563172 ChEMBL	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 ChEMBL	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 ChEMBL	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 ChEMBL	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 ZINC	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 ZINC	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 ZINC	1.000	458.5 Da LogP -0.88 TPSA 123.5	1 viol.	✓ Clean	`OCCOCCOCCOCCOCCOCCOCCOCCOCCOCCO`
ZINC1282589 ZINC	1.000	360.4 Da LogP 2.01 TPSA 77.3	✓ Ro5	Alert	`O=C1C(N2CCOCC2)=C(n2nnc3ccccc32)C(=O)c2ccccc21`
ZINC1529498 ZINC	1.000	200.3 Da LogP 3.99 TPSA 37.3	✓ Ro5	✓ Clean	`CCCCCCCCCCCC(=O)O`
ZINC1530417 ZINC	1.000	228.4 Da LogP 4.77 TPSA 37.3	✓ Ro5	✓ Clean	`CCCCCCCCCCCCCC(=O)O`
ZINC1628119 ZINC	1.000	214.3 Da LogP 4.38 TPSA 37.3	✓ Ro5	✓ Clean	`CCCCCCCCCCCCC(=O)O`
ZINC3874716 ZINC	1.000	414.5 Da LogP -0.90 TPSA 114.3	✓ Ro5	✓ Clean	`OCCOCCOCCOCCOCCOCCOCCOCCOCCO`
ZINC4283769 ZINC	1.000	238.3 Da LogP -0.96 TPSA 77.4	✓ Ro5	✓ Clean	`OCCOCCOCCOCCOCCO`
ZINC4521548 ZINC	1.000	282.3 Da LogP -0.95 TPSA 86.6	✓ Ro5	✓ Clean	`OCCOCCOCCOCCOCCOCCO`
ZINC5178829 ZINC	1.000	326.4 Da LogP -0.93 TPSA 95.8	✓ Ro5	✓ Clean	`OCCOCCOCCOCCOCCOCCOCCO`
ZINC5178830 ZINC	1.000	370.4 Da LogP -0.91 TPSA 105.1	✓ Ro5	✓ Clean	`OCCOCCOCCOCCOCCOCCOCCOCCO`
ZINC100822378 ZINC	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 ZINC	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 ZINC	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 ZINC	0.850	228.3 Da LogP 3.56 TPSA 54.4	✓ Ro5	✓ Clean	`CCCCCCCC(=O)CCCCC(=O)O`
ZINC138458029 ZINC	0.850	228.3 Da LogP 3.56 TPSA 54.4	✓ Ro5	✓ Clean	`CCCCCCC(=O)CCCCCC(=O)O`
ZINC144395054 ZINC	0.850	242.4 Da LogP 3.95 TPSA 54.4	✓ Ro5	✓ Clean	`CCCCCC(=O)CCCCCCCC(=O)O`
ZINC14619628 ZINC	0.850	270.4 Da LogP 4.73 TPSA 54.4	✓ Ro5	✓ Clean	`CCCCCC(=O)CCCCCCCCCC(=O)O`
ZINC196749828 ZINC	0.850	214.3 Da LogP 3.17 TPSA 54.4	✓ Ro5	✓ Clean	`CCCCCCC(=O)CCCCC(=O)O`
ZINC2113934076 ZINC	0.850	256.4 Da LogP 4.34 TPSA 54.4	✓ Ro5	✓ Clean	`CCCCCCC(=O)CCCCCCCC(=O)O`
ZINC2113934082 ZINC	0.850	256.4 Da LogP 4.34 TPSA 54.4	✓ Ro5	✓ Clean	`CCCCCCCC(=O)CCCCCCC(=O)O`
ZINC2113934083 ZINC	0.850	256.4 Da LogP 4.34 TPSA 54.4	✓ Ro5	✓ Clean	`CCCCCCCCCC(=O)CCCCC(=O)O`
ZINC2243670 ZINC	0.850	228.3 Da LogP 3.56 TPSA 54.4	✓ Ro5	✓ Clean	`CCCCCC(=O)CCCCCCC(=O)O`
ZINC2569203 ZINC	0.850	214.3 Da LogP 3.17 TPSA 54.4	✓ Ro5	✓ Clean	`CCCCCC(=O)CCCCCC(=O)O`
ZINC4798470 ZINC	0.850	270.4 Da LogP 4.73 TPSA 54.4	✓ Ro5	✓ Clean	`CCCCCCC(=O)CCCCCCCCC(=O)O`
ZINC5973005 ZINC	0.850	242.4 Da LogP 3.95 TPSA 54.4	✓ Ro5	✓ Clean	`CCCCCCC(=O)CCCCCCC(=O)O`
ZINC71418182 ZINC	0.850	270.4 Da LogP 4.73 TPSA 54.4	✓ Ro5	✓ Clean	`CCCCCCCCCCC(=O)CCCCC(=O)O`
ZINC79244776 ZINC	0.850	270.4 Da LogP 4.73 TPSA 54.4	✓ Ro5	✓ Clean	`CCCCCCCC(=O)CCCCCCCC(=O)O`
ZINC86037082 ZINC	0.850	270.4 Da LogP 4.73 TPSA 54.4	✓ Ro5	✓ Clean	`CCCCCCCCCC(=O)CCCCCC(=O)O`
ZINC86037089 ZINC	0.850	270.4 Da LogP 4.73 TPSA 54.4	✓ Ro5	✓ Clean	`CCCCCCCCC(=O)CCCCCCC(=O)O`
ZINC86039283 ZINC	0.850	242.4 Da LogP 3.95 TPSA 54.4	✓ Ro5	✓ Clean	`CCCCCCCCC(=O)CCCCC(=O)O`
ZINC100919209 ZINC	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 ZINC	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 ZINC	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 ZINC	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 ZINC	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 ZINC	0.810	214.3 Da LogP 3.17 TPSA 54.4	✓ Ro5	✓ Clean	`CCCCCCCC(=O)CCCC(=O)O`
ZINC4582907 ZINC	0.810	200.3 Da LogP 2.78 TPSA 54.4	✓ Ro5	✓ Clean	`CCCCCCC(=O)CCCC(=O)O`
ZINC4727003 ZINC	0.810	312.4 Da LogP 4.69 TPSA 71.4	✓ Ro5	✓ Clean	`CCCCCCC(=O)CCC(=O)CCCCCCCC(=O)O`
ZINC86037074 ZINC	0.810	270.4 Da LogP 4.73 TPSA 54.4	✓ Ro5	✓ Clean	`CCCCCCCCCCCC(=O)CCCC(=O)O`
ZINC102205938 ZINC	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 ZINC	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 ZINC	0.800	200.3 Da LogP 2.78 TPSA 54.4	✓ Ro5	✓ Clean	`CCCCCC(=O)CCCCC(=O)O`
ZINC100478511 ZINC	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 ZINC	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 ZINC	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 ZINC	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 ZINC	0.773	435.5 Da LogP 3.50 TPSA 71.3	✓ Ro5	Alert	`O=C1C(N2CCN(c3ccccc3)CC2)=C(n2nnc3ccccc32)C(=O)…`
ZINC100919212 ZINC	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.

VK055_2849

Target candidate with partial support; inspect missing evidence before prioritizing.

Main supporting evidence

Risks to review

Evidence gaps

Prioritization evidence

Off-target risk

Essentiality

Localization

Structure confidence

Binding-site evidence

Cross-references

Sequence

Chemistry

Sequence

Functional annotations

Enzyme Commission (EC)

Gene Ontology (GO)

Sequence domains and features

3D structure

Binding pockets · P2Rank

Binding pockets · FPocket

Binding pockets · P2Rank

Structural evidence

Ligand evidence