Protein profile

KP13_01236

Bifunctional 2',3'-cyclic-nucleotide 2'-phosphodiesterase/3'-nucleotidase

Genome: KpKP13

Gene: AHE46699.1 cpdB Structure source: Experimental + ColabFold UniProt A6THC4
Amino acids 647
Annotations 7
Features 43
PDB binders 9
Druggability 0.579

Overview

Basic information about this protein and its source genome.

Accession
KP13_01236
Gene
AHE46699.1 cpdB
Status
annotated
Amino acids
647
Structure source
Experimental + ColabFold

Target profile

Computed evidence for target prioritization.

Human off-target
hit
Human identity (%)
26.778
Human E-value
3.01e-08
Gut microbiome off-target
hit
Essential (DEG)
Y
DEG identity (%)
62.366
DEG E-value
0.0
Localization
Periplasmic
ColabFold pLDDT
93.96

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 0.579
Structure 3JYF
Pocket Pocket 1
P2Rank 0.434
Structure 3JYF
Pocket Pocket 1
ColabFold model
FPocket 0.975 · Pocket 25
P2Rank 0.994 · Pocket 1
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 145 / 4744 genomes with a hit
Normalized 0.031

Sequence

Primary amino-acid sequence viewer.

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

7 GO

Gene Ontology (GO)

7
  • GO:0009166 The chemical reactions and pathways resulting in the breakdown of nucleotides, any nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the glycose moiety; may be mono-, di- or triphosphate; this definition includes cyclic-nucleotides (nucleoside cyclic phosphates).
  • GO:0009117 The chemical reactions and pathways involving a nucleotide, a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the glycose moiety; may be mono-, di- or triphosphate; this definition includes cyclic nucleotides (nucleoside cyclic phosphates).
  • GO:0016787 Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc.
  • GO:0008663 Catalysis of the reaction: nucleoside 2',3'-cyclic phosphate + H2O = nucleoside 3'-phosphate.
  • GO:0046872 Binding to a metal ion.
  • GO:0016788 Catalysis of the hydrolysis of any ester bond.
  • GO:0000166 Binding to a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.

Sequence Features

Domain/signature hits from InterPro and related databases.

43 records
Show feature table
Start End DB Term Name
1 19 SignalP_GRAM_NEGATIVE SignalP-noTM SignalP-noTM
20 647 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
4 14 Phobius SIGNAL_PEPTIDE_H_REGION Hydrophobic region of a signal peptide.
19 353 SUPERFAMILY SSF56300 Metallo-dependent phosphatases
19 353 InterPro IPR029052 Metallo-dependent phosphatase-like
22 647 NCBIfam TIGR01390 2',3'-cyclic-nucleotide 2'-phosphodiesterase
22 647 InterPro IPR006294 2',3'-cyclic-nucleotide 2'-phosphodiesterase/3'-nucleotidase
1 3 Phobius SIGNAL_PEPTIDE_N_REGION N-terminal region of a signal peptide.
363 594 FunFam G3DSA:3.90.780.10:FF:000002 Bifunctional 2',3'-cyclic-nucleotide 2'-phosphodiesterase/3'-nucleotidase
355 597 SUPERFAMILY SSF55816 5'-nucleotidase (syn. UDP-sugar hydrolase), C-terminal domain
355 597 InterPro IPR036907 5'-Nucleotidase, C-terminal domain superfamily
14 595 PANTHER PTHR11575 5'-NUCLEOTIDASE-RELATED
14 595 InterPro IPR006179 5'-Nucleotidase/apyrase
356 550 Pfam PF02872 5'-nucleotidase, C-terminal domain
356 550 InterPro IPR008334 5'-Nucleotidase, C-terminal
1 19 SignalP_GRAM_POSITIVE SignalP-TM SignalP-TM
365 594 Gene3D G3DSA:3.90.780.10 -
365 594 InterPro IPR036907 5'-Nucleotidase, C-terminal domain superfamily
24 259 Pfam PF00149 Calcineurin-like phosphoesterase
24 259 InterPro IPR004843 Calcineurin-like phosphoesterase domain, ApaH type
530 549 PRINTS PR01607 Apyrase family signature
530 549 InterPro IPR006179 5'-Nucleotidase/apyrase
243 266 PRINTS PR01607 Apyrase family signature
243 266 InterPro IPR006179 5'-Nucleotidase/apyrase
283 303 PRINTS PR01607 Apyrase family signature
283 303 InterPro IPR006179 5'-Nucleotidase/apyrase
22 40 PRINTS PR01607 Apyrase family signature
22 40 InterPro IPR006179 5'-Nucleotidase/apyrase
215 232 PRINTS PR01607 Apyrase family signature
215 232 InterPro IPR006179 5'-Nucleotidase/apyrase
428 451 PRINTS PR01607 Apyrase family signature
428 451 InterPro IPR006179 5'-Nucleotidase/apyrase
1 19 Phobius SIGNAL_PEPTIDE Signal peptide region
24 36 ProSitePatterns PS00785 5'-nucleotidase signature 1.
24 36 InterPro IPR006146 5'-Nucleotidase, conserved site
109 120 ProSitePatterns PS00786 5'-nucleotidase signature 2.
109 120 InterPro IPR006146 5'-Nucleotidase, conserved site
15 19 Phobius SIGNAL_PEPTIDE_C_REGION C-terminal region of a signal peptide.
16 354 Gene3D G3DSA:3.60.21.10 -
16 354 InterPro IPR029052 Metallo-dependent phosphatase-like
16 354 FunFam G3DSA:3.60.21.10:FF:000037 Bifunctional 2',3'-cyclic-nucleotide 2'-phosphodiesterase/3'-nucleotidase
24 321 CDD cd07410 MPP_CpdB_N
24 321 InterPro IPR041827 CpdB, N-terminal metallophosphatase 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 3JYF
X-ray 20.00 Å - Viewing
ColabFold KP13_01236
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
27 0.506
1 0.273
4 0.222

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 15.55 0.756
2 5.44 0.259
3 4.95 0.224
4 1.46 0.02

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

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.

Show only:
Ligand Source crystal MW · LogP · TPSA Lipinski PAINS SMILES
TAM 163.2 Da LogP -1.17 TPSA 86.7 ✓ Ro5 ✓ Clean C(CO)C(CCO)(CCO)N

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.