Protein profile

KP13_31499

Cytidylate kinase

Genome: KpKP13

Gene: cmk AHE45430.1 Structure source: AlphaFold + ColabFold UniProt A0A0H3GL15
Export view
Amino acids 227
Annotations 9
Features 15
PDB binders 3
Druggability 0.592

Overview

Basic information about this protein and its source genome.

Accession
KP13_31499
Assembly
Klebsiella pneumoniae subsp. pneumoniae Kp13, complete sequence
Gene
cmk AHE45430.1
Status
annotated
Amino acids
227
Structure source
AlphaFold + ColabFold
EC
2.7.4.25
GO
GO:0005524 Binding to ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator. GO:0004127 OBSOLETE. Catalysis of the reaction: ATP + (d)CMP = ADP + (d)CDP. GO:0006139 Any cellular metabolic process involving nucleobases, nucleosides, nucleotides and nucleic acids. GO:0005829 The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes. GO:0036430 Catalysis of the reaction: ATP + CMP = ADP + CDP. GO:0036431 Catalysis of the reaction: ATP + dCMP = ADP + dCDP.

Target profile

Computed evidence for target prioritization.

Human off-target
No hit
Human identity (%)
0.0
Gut microbiome off-target
hit
Essential (DEG)
Y
DEG identity (%)
90.308
DEG E-value
2.19e-150
Localization
Cytoplasmic
ColabFold pLDDT
93.15

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 0.592
Structure A0A0H3GL15
Pocket Pocket 5
P2Rank 0.926
Structure A0A0H3GL15
Pocket Pocket 1
ColabFold model
FPocket 0.581 · Pocket 2
P2Rank 0.901 · Pocket 1
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 217 / 4744 genomes with a hit
Normalized 0.046

Sequence

Primary amino-acid sequence viewer.

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 8 GO

Enzyme Commission (EC)

1

Gene Ontology (GO)

8
  • GO:0005524 Binding to ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
  • GO:0004127 OBSOLETE. Catalysis of the reaction: ATP + (d)CMP = ADP + (d)CDP.
  • GO:0006139 Any cellular metabolic process involving nucleobases, nucleosides, nucleotides and nucleic acids.
  • GO:0005829 The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
  • GO:0036430 Catalysis of the reaction: ATP + CMP = ADP + CDP.
  • GO:0036431 Catalysis of the reaction: ATP + dCMP = ADP + dCDP.
  • GO:0015949 The chemical reactions and pathways by which a nucleobase, nucleoside or nucleotide small molecule is synthesized from another nucleobase, nucleoside or nucleotide small molecule.
  • GO:0006220 The chemical reactions and pathways involving a pyrimidine nucleotide, a compound consisting of nucleoside (a pyrimidine base linked to a deoxyribose or ribose sugar) esterified with a phosphate group at either the 3' or 5'-hydroxyl group of the sugar.

Sequence Features

Domain/signature hits from InterPro and related databases.

15 records
Show feature table
Start End DB Term Name
7 205 CDD cd02020 CMPK
7 205 InterPro IPR011994 Cytidylate kinase domain
1 227 Gene3D G3DSA:3.40.50.300 -
1 227 InterPro IPR027417 P-loop containing nucleoside triphosphate hydrolase
4 215 PANTHER PTHR21299 CYTIDYLATE KINASE/PANTOATE-BETA-ALANINE LIGASE
8 221 Pfam PF02224 Cytidylate kinase
8 221 InterPro IPR011994 Cytidylate kinase domain
6 224 Hamap MF_00238 Cytidylate kinase [cmk].
6 224 InterPro IPR003136 Cytidylate kinase
202 222 Coils Coil Coil
1 227 FunFam G3DSA:3.40.50.300:FF:000262 Cytidylate kinase
6 224 SUPERFAMILY SSF52540 P-loop containing nucleoside triphosphate hydrolases
6 224 InterPro IPR027417 P-loop containing nucleoside triphosphate hydrolase
6 219 NCBIfam TIGR00017 (d)CMP kinase
6 219 InterPro IPR003136 Cytidylate kinase

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

Loading 3D structure...

Legend High Medium Low

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_A0A0H3GL15
AlphaFold — — full sequence — Viewing
ColabFold KP13_31499
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 0.592
1 0.402
13 0.377
6 0.007

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 34.41 0.926
2 0.85 0.003

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.

53 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
CAR
1KDR
P0A6I0 323.2 Da LogP -2.45 TPSA 177.4 ✓ Ro5 ✓ Clean C1=CN(C(=O)N=C1N)[C@H]2[C@H]([C@@H]([C@H](O2)CO…
DC
2FEO
P0A6I0 307.2 Da LogP -1.42 TPSA 157.1 ✓ Ro5 ✓ Clean C1[C@@H]([C@H](O[C@H]1N2C=CC(=NC2=O)N)COP(=O)(O…
DOC
1KDT
P0A6I0 291.2 Da LogP -0.39 TPSA 136.9 ✓ Ro5 ✓ Clean C1C[C@@H](O[C@@H]1COP(=O)(O)O)N2C=CC(=NC2=O)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.