Protein target profile

VK055_0143

FAD dependent oxidoreductase family protein

Genome: KpATCC43816 Gene: AIK78771.1 3D evidence: AlphaFold DB model + ColabFold model UniProt A0A0H3GRR7
Length 423
Pocket druggability 0.934
Direct ligand evidence 0 59 total records
Functional annotation 0 EC 3 GO
Target summary

Promising target candidate with multiple supporting evidence streams.

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 (%)
23.148 Lower values reduce human off-target concern.
Human E-value
7.43e-08
Gut microbiome similarity
3.3% of screened genomes Lower prevalence suggests narrower overlap with the screened gut microbiome.

Essentiality

Essential (DEG)
Y
DEG identity (%)
88.889 Higher values support similarity to known essential genes.
DEG E-value
0.0 Smaller values mean stronger essential-gene similarity.

Localization

Localization
CytoplasmicMembrane

Structure confidence

ColabFold pLDDT
93.02 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 0.934
Structure A0A0H3GRR7
Pocket Pocket 2
P2Rank 0.988
Structure A0A0H3GRR7
Pocket Pocket 1
ColabFold model
FPocket 0.453 · Pocket 19
P2Rank 0.993 · Pocket 1
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 157 / 4744 genomes with a hit
Prevalence 3.3%

Cross-references

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

Sequence

Primary amino-acid sequence viewer.

MVGVASAWYLSQAGHDVTVIDRQPGPAEETSAANAGQISPGYAAPWAAPGVPLKAIKWMFQRHAPLAIGLDGTSFQLKWMWQMLRNCDTRHYMENKGRMVRLAEYSRDCLKALRDTTGIQYEGRQGGTLQLFRTAKQYENATRDIAVLEDAGVPYQLLEAKRLAEVEPALAEVSHKLTGGLRLPNDETGDCQLFTTRLAAMAEQAGVTFRFNTAVDALLHEGDRIAGVKCGDEIIKGDAYVMAFGSYSTAMLKGLVDIPVYPLKGYSLTIPIAQEDGAPVSTILDETYKIAITRFDQRIRVGGMAEIVGFNKALLQPRRETLEMVVRDLFPRGGHVEQATFWTGLRPMTPDGTPVVGRTAYKNLWLNTGHGTLGWTMACGSGQLISDLISGRTPAIPYDDLAVARYSPGFTPARPQHLHGAHN

Functional annotations

Enzyme classification and Gene Ontology terms linked to this protein.

3 GO

Gene Ontology (GO)

3
  • GO:0019478 The chemical reactions and pathways resulting in the breakdown of D-amino acids, the D-enantiomers of amino acids.
  • GO:0016491 Catalysis of an oxidation-reduction (redox) reaction, a reversible chemical reaction in which the oxidation state of an atom or atoms within a molecule is altered. One substrate acts as a hydrogen or electron donor and becomes oxidized, while the other acts as hydrogen or electron acceptor and becomes reduced.
  • GO:0008718 Catalysis of the reaction: a D-alpha-amino acid + a quinone + H2O = a 2-oxocarboxylate + a quinol + NH4+.

Sequence domains and features

Domain and signature matches imported from InterPro and related databases.

14 records
Show feature table
Start End DB Term Name
1 401 Hamap MF_01202 D-amino acid dehydrogenase [dadA].
1 401 InterPro IPR023080 D-amino acid dehydrogenase DadA
2 53 Gene3D G3DSA:3.50.50.60 -
2 53 InterPro IPR036188 FAD/NAD(P)-binding domain superfamily
260 350 SUPERFAMILY SSF54373 FAD-linked reductases, C-terminal domain
125 353 Gene3D G3DSA:3.30.9.10 -
2 410 SUPERFAMILY SSF51905 FAD/NAD(P)-binding domain
2 410 InterPro IPR036188 FAD/NAD(P)-binding domain superfamily
96 394 Gene3D G3DSA:3.50.50.60 -
96 394 InterPro IPR036188 FAD/NAD(P)-binding domain superfamily
2 405 PANTHER PTHR13847 SARCOSINE DEHYDROGENASE-RELATED
1 388 Pfam PF01266 FAD dependent oxidoreductase
1 388 InterPro IPR006076 FAD dependent oxidoreductase
1 53 FunFam G3DSA:3.50.50.60:FF:000020 D-amino acid dehydrogenase

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.

Download VMD script Full viewer

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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 · FPocket

Druggability: high ≥ 0.7 · medium 0.4–0.69 · low < 0.4

Site 1 FPocket #2
0.934
Likely same site as P2Rank 1 8.0 Å 51 shared residues 82% of smaller site
Unusual size
Show in viewer
Surrounding area
Site 2 FPocket #14
0.23
Unusual size
Show in viewer
Surrounding area

Binding pockets · P2Rank

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

Site 1 P2Rank #1
0.988
Likely same site as FPocket 2 8.0 Å 51 shared residues 82% of smaller site
Show in viewer
Surrounding area
Site 2 P2Rank #2
0.394
Show in viewer
Surrounding area
Site 3 P2Rank #3
0.235
Show in viewer
Surrounding area
Site 4 P2Rank #4
0.162
Show in viewer
Surrounding area
Site 5 P2Rank #5
0.144
Show in viewer
Surrounding area
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_A0A0H3GRR7
AlphaFold DB full sequence Viewing
ColabFold VK055_0143
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.

59 records
Chemistry signal

Structural ligand evidence is available for this target.

Direct evidence 0 same-protein records
Transferred evidence 9 records from similar proteins
Structural ligands 9 0 loaded crystals
Measured bioactivity 0 direct and transferred ChEMBL records
Proposed compounds 50 similarity-based ZINC candidates
Best available ligand signal
AAC PDB via homolog 117.1 Da · LogP -0.79 · TPSA 66.4 Open detail RCSB PDB
B6X PDB via homolog Detail RCSB PDB
DMG PDB via homolog Detail RCSB PDB
FOA PDB via homolog Detail RCSB PDB
FON PDB via homolog Detail RCSB PDB

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.

Show only:
Ligand Source crystal UniProt (homolog) MW · LogP · TPSA Lipinski PAINS SMILES
AAC RCSB PDB O31616 117.1 Da LogP -0.79 TPSA 66.4 ✓ Ro5 ✓ Clean CC(=O)NCC(=O)O
B6X RCSB PDB X5IYZ1 248.3 Da LogP 2.62 TPSA 74.6 ✓ Ro5 ✓ Clean CCCCCC[C@H](CC(=O)O)SCC(=O)O
DMG RCSB PDB Q50LF2 103.1 Da LogP -0.37 TPSA 40.5 ✓ Ro5 ✓ Clean CN(C)CC(=O)O
FOA RCSB PDB Q3ZDR0 112.1 Da LogP 0.98 TPSA 50.4 ✓ Ro5 ✓ Clean c1cc(oc1)C(=O)O
FON RCSB PDB Q50LF2 473.4 Da LogP -0.73 TPSA 219.8 1 viol. ✓ Clean c1cc(ccc1C(=O)N[C@@H](CCC(=O)O)C(=O)O)NC[C@@H]2…
GOA RCSB PDB O31616 76.1 Da LogP -0.94 TPSA 57.5 ✓ Ro5 ✓ Clean C(C(=O)O)O
MTG RCSB PDB Q50LF2 105.1 Da LogP -0.90 TPSA 40.1 ✓ Ro5 ✓ Clean CSCC(=O)[O-]
PEO RCSB PDB O31616 34.0 Da LogP 0.02 TPSA 40.5 ✓ Ro5 ✓ Clean OO
PYC RCSB PDB Q50LF2 110.1 Da LogP -0.62 TPSA 55.9 ✓ Ro5 ✓ Clean c1cc([nH]c1)C(=O)[O-]

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.