Protein profile

KP13_02076

Nuclease sbcCD subunit D

Genome: KpKP13

Gene: sbcD AHE46079.1 Structure source: AlphaFold + ColabFold UniProt A0A0H3GJ04
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Amino acids 401
Annotations 6
Features 14
PDB binders 7
Druggability 0.691

Overview

Basic information about this protein and its source genome.

Accession
KP13_02076
Assembly
Klebsiella pneumoniae subsp. pneumoniae Kp13, complete sequence
Gene
sbcD AHE46079.1
Status
annotated
Amino acids
401
Structure source
AlphaFold + ColabFold
GO
GO:0004519 Catalysis of the cleavage of ester linkages within nucleic acids by creating internal breaks. GO:0006259 Any cellular metabolic process involving deoxyribonucleic acid. This is one of the two main types of nucleic acid, consisting of a long, unbranched macromolecule formed from one, or more commonly, two, strands of linked deoxyribonucleotides. GO:0016787 Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. GO:0008408 Catalysis of the hydrolysis of ester linkages within nucleic acids by removing nucleotide residues from the 3' end. GO:0006310 Any process in which a new genotype is formed by reassortment of genes resulting in gene combinations different from those that were present in the parents. In eukaryotes genetic recombination can occur by chromosome assortment, intrachromosomal recombination, or nonreciprocal interchromosomal recombination. Interchromosomal recombination occurs by crossing over. In bacteria it may occur by genetic transformation, conjugation, transduction, or F-duction. GO:0006260 The cellular metabolic process in which a cell duplicates one or more molecules of DNA. DNA replication begins when specific sequences, known as origins of replication, are recognized and bound by the origin recognition complex, and ends when the original DNA molecule has been completely duplicated and the copies topologically separated. The unit of replication usually corresponds to the genome of the cell, an organelle, or a virus. The template for replication can either be an existing DNA molecule or RNA.

Target profile

Computed evidence for target prioritization.

Human off-target
No hit
Human identity (%)
0.0
Gut microbiome off-target
hit
Essential (DEG)
N
DEG identity (%)
0.0
Localization
Cytoplasmic
ColabFold pLDDT
91.61

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 0.691
Structure A0A0H3GJ04
Pocket Pocket 5
P2Rank 0.063
Structure A0A0H3GJ04
Pocket Pocket 1
ColabFold model
FPocket 0.594 · Pocket 4
P2Rank 0.06 · Pocket 1
Core conservation Accessory gene
Roary core
CoreCruncher accessory
Gut microbiome 109 / 4744 genomes with a hit
Normalized 0.023

Sequence

Primary amino-acid sequence viewer.

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

6 GO

Gene Ontology (GO)

6
  • GO:0004519 Catalysis of the cleavage of ester linkages within nucleic acids by creating internal breaks.
  • GO:0006259 Any cellular metabolic process involving deoxyribonucleic acid. This is one of the two main types of nucleic acid, consisting of a long, unbranched macromolecule formed from one, or more commonly, two, strands of linked deoxyribonucleotides.
  • GO:0016787 Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc.
  • GO:0008408 Catalysis of the hydrolysis of ester linkages within nucleic acids by removing nucleotide residues from the 3' end.
  • GO:0006310 Any process in which a new genotype is formed by reassortment of genes resulting in gene combinations different from those that were present in the parents. In eukaryotes genetic recombination can occur by chromosome assortment, intrachromosomal recombination, or nonreciprocal interchromosomal recombination. Interchromosomal recombination occurs by crossing over. In bacteria it may occur by genetic transformation, conjugation, transduction, or F-duction.
  • GO:0006260 The cellular metabolic process in which a cell duplicates one or more molecules of DNA. DNA replication begins when specific sequences, known as origins of replication, are recognized and bound by the origin recognition complex, and ends when the original DNA molecule has been completely duplicated and the copies topologically separated. The unit of replication usually corresponds to the genome of the cell, an organelle, or a virus. The template for replication can either be an existing DNA molecule or RNA.

Sequence Features

Domain/signature hits from InterPro and related databases.

14 records
Show feature table
Start End DB Term Name
1 225 Pfam PF00149 Calcineurin-like phosphoesterase
1 225 InterPro IPR004843 Calcineurin-like phosphoesterase domain, ApaH type
276 372 Pfam PF12320 Type 5 capsule protein repressor C-terminal domain
276 372 InterPro IPR026843 Nuclease SbcCD subunit D, C-terminal domain
277 340 Gene3D G3DSA:3.30.160.720 -
1 335 SUPERFAMILY SSF56300 Metallo-dependent phosphatases
1 335 InterPro IPR029052 Metallo-dependent phosphatase-like
2 247 CDD cd00840 MPP_Mre11_N
2 247 InterPro IPR041796 Mre11 nuclease, N-terminal metallophosphatase domain
1 276 Gene3D G3DSA:3.60.21.10 -
1 276 InterPro IPR029052 Metallo-dependent phosphatase-like
1 395 PANTHER PTHR30337 COMPONENT OF ATP-DEPENDENT DSDNA EXONUCLEASE
1 253 NCBIfam TIGR00619 exonuclease subunit SbcD
1 253 InterPro IPR004593 Nuclease SbcCD subunit D

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

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_A0A0H3GJ04
AlphaFold — — full sequence — Viewing
ColabFold KP13_02076
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
5 0.691

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 1.34 0.015
2 1.14 0.009

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.

57 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
2PK
4O4K
Q9X1X0 220.3 Da LogP 1.53 TPSA 73.2 ✓ Ro5 ✓ Clean [H]/N=C\1/NC(=O)/C(=C\c2ccc(cc2)O)/S1
2PV
4O5G
Q9X1X0 219.3 Da LogP 1.41 TPSA 79.0 ✓ Ro5 ✓ Clean [H]/N=C\1/NC(=O)/C(=C\c2ccc(cc2)N)/S1
2PW
4O43
Q9X1X0 293.4 Da LogP 3.39 TPSA 40.5 ✓ Ro5 Alert CC[C@@H](C)N1C(=O)/C(=C\c2ccc(cc2)O)/SC1=S
2Q0
4O24
Q9X1X0 293.4 Da LogP 3.25 TPSA 40.5 ✓ Ro5 Alert CC(C)CN1C(=O)/C(=C/c2ccc(cc2)O)/SC1=S
BU7
6ASC
Q9X1X0 293.4 Da LogP 3.39 TPSA 40.5 ✓ Ro5 Alert CCCCN1C(=O)/C(=C\c2ccc(cc2)O)/SC1=S
UKV
6X1Y
Q9X1X0 251.3 Da LogP 2.18 TPSA 38.3 ✓ Ro5 Alert COc1cccc(c1)/C=C\2/C(=O)NC(=S)S2
UL1
6X1Z
Q9X1X0 281.4 Da LogP 2.19 TPSA 47.6 ✓ Ro5 Alert COc1ccc(cc1OC)/C=C\2/C(=O)NC(=S)S2

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.