Protein profile

VK055_4939

cytidine deaminase

Genome: KpATCC43816

Gene: cdd AIK83465.1 Structure source: Experimental + ColabFold UniProt A6TBN1
Amino acids 286
Annotations 5
Features 26
PDB binders 9
Druggability 0.587

Overview

Basic information about this protein and its source genome.

Accession
VK055_4939
Gene
cdd AIK83465.1
Status
annotated
Amino acids
286
Structure source
Experimental + ColabFold

Target profile

Computed evidence for target prioritization.

Human off-target
hit
Human identity (%)
33.036
Human E-value
8.75e-10
Gut microbiome off-target
hit
Essential (DEG)
Y
DEG identity (%)
51.19
DEG E-value
1.63e-82
Localization
Unknown
ColabFold pLDDT
98.21

Selected Druggability evidence

PDB experimental structure

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 0.587
Structure 6K63
Pocket Pocket 3
P2Rank 0.479
Structure 6K63
Pocket Pocket 1
ColabFold model
FPocket 0.615 · Pocket 5
P2Rank 0.338 · Pocket 1
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 123 / 4744 genomes with a hit
Normalized 0.026

Sequence

Primary amino-acid sequence viewer.

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

5 GO

Gene Ontology (GO)

5
  • GO:0003824 Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
  • GO:0004126 Catalysis of the reaction: cytidine + H+ + H2O = uridine + NH4 and deoxycytidine + H+ + H2O = deoxyuridine + NH4+.
  • GO:0008270 Binding to a zinc ion (Zn).
  • GO:0009972 OBSOLETE. The removal of amino group in the presence of water.
  • GO:0016787 Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc.

Sequence Features

Domain/signature hits from InterPro and related databases.

26 records
Show feature table
Start End DB Term Name
172 286 Gene3D G3DSA:3.40.140.10 Cytidine Deaminase, domain 2
1 284 Hamap MF_01558 Cytidine deaminase [cdd].
1 284 InterPro IPR020797 Cytidine deaminase, bacteria
178 286 ProSiteProfiles PS51747 Cytidine and deoxycytidylate deaminases domain profile.
178 286 InterPro IPR002125 Cytidine and deoxycytidylate deaminase domain
144 285 SUPERFAMILY SSF53927 Cytidine deaminase-like
144 285 InterPro IPR016193 Cytidine deaminase-like
61 144 CDD cd01283 cytidine_deaminase
94 128 ProSitePatterns PS00903 Cytidine and deoxycytidylate deaminases zinc-binding region signature.
94 128 InterPro IPR016192 APOBEC/CMP deaminase, zinc-binding
180 226 PANTHER PTHR11644 CYTIDINE DEAMINASE
23 276 NCBIfam TIGR01355 cytidine deaminase
23 276 InterPro IPR006263 Cytidine deaminase, homodimeric
177 284 FunFam G3DSA:3.40.140.10:FF:000006 Cytidine deaminase
6 141 SUPERFAMILY SSF53927 Cytidine deaminase-like
6 141 InterPro IPR016193 Cytidine deaminase-like
40 160 ProSiteProfiles PS51747 Cytidine and deoxycytidylate deaminases domain profile.
40 160 InterPro IPR002125 Cytidine and deoxycytidylate deaminase domain
6 285 PIRSF PIRSF006334 Cdd_plus_pseudo
185 244 CDD cd01283 cytidine_deaminase
52 131 Pfam PF00383 Cytidine and deoxycytidylate deaminase zinc-binding region
52 131 InterPro IPR002125 Cytidine and deoxycytidylate deaminase domain
21 171 FunFam G3DSA:3.40.140.10:FF:000007 Cytidine deaminase
21 171 Gene3D G3DSA:3.40.140.10 Cytidine Deaminase, domain 2
149 268 Pfam PF08211 Cytidine and deoxycytidylate deaminase zinc-binding region
149 268 InterPro IPR013171 Cytidine/deoxycytidylate deaminase, zinc-binding domain

3D Structure

Selected loaded structure. Experimental PDB entries may cover only a portion of the sequence; predicted models typically cover the full protein.

3D visualization script Full viewer

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Structural evidence

1 + 1

Experimental PDB entries and predicted models. Click Switch to display a different structure in the viewer.

Entry Method Resolution Chain Coverage Links Status
PDB 6K63
X-ray 20.00 Å - Viewing
ColabFold VK055_4939
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 0.953
4 0.776
2 0.697

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 90.71 0.995
2 23.46 0.889
3 23.22 0.887
4 7.16 0.372
5 6.17 0.307

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.

75 records

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
CTD P0ABF6 242.2 Da LogP -1.96 TPSA 117.9 ✓ Ro5 ✓ Clean C1=CN(C(=O)C=C1N)[C@H]2[C@@H]([C@@H]([C@H](O2)C…
CTN P56389 243.2 Da LogP -2.56 TPSA 130.8 ✓ Ro5 ✓ Clean C1=CN(C(=O)N=C1N)[C@H]2[C@@H]([C@@H]([C@H](O2)C…
DHZ P0ABF6 230.2 Da LogP -2.04 TPSA 102.3 ✓ Ro5 ✓ Clean C1C=CN(C(=O)N1)[C@H]2[C@@H]([C@@H]([C@H](O2)CO)…
NH3 P56389 17.0 Da LogP 0.16 TPSA 35.0 ✓ Ro5 ✓ Clean N
THU P19079 230.2 Da LogP -1.60 TPSA 99.1 ✓ Ro5 ✓ Clean C1CN(C(=O)NC1=O)C2C[C@@H]([C@H](O2)CO)O
TYU P56389 248.2 Da LogP -2.84 TPSA 122.5 ✓ Ro5 ✓ Clean C1CN(C(=O)N[C@@H]1O)[C@H]2[C@@H]([C@@H]([C@H](O…
URD P56389 243.2 Da LogP -2.26 TPSA 107.3 ✓ Ro5 ✓ Clean C1C(=O)C=CN(C1=O)[C@H]2[C@@H]([C@@H]([C@H](O2)C…
URI P56389 244.2 Da LogP -2.85 TPSA 124.8 ✓ Ro5 ✓ Clean C1=CN(C(=O)NC1=O)[C@H]2[C@@H]([C@@H]([C@H](O2)C…
ZEB P0ABF6 246.2 Da LogP -2.72 TPSA 122.5 ✓ Ro5 ✓ Clean C1=CN(C(=O)N[C@@H]1O)C2[C@@H]([C@@H]([C@H](O2)C…

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.