Protein profile

VK055_3461

CDP-diacylglycerol pyrophosphatase

Genome: KpATCC43816

Gene: AIK82017.1 cdh Structure source: AlphaFold + ColabFold UniProt A0A0H3H083
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Amino acids 254
Annotations 6
Features 19
PDB binders 0
Druggability 0.459

Overview

Basic information about this protein and its source genome.

Accession
VK055_3461
Assembly
Klebsiella pneumoniae subsp. pneumoniae strain ATCC 43816 KPPR1, complete genome
Gene
AIK82017.1 cdh
Status
annotated
Amino acids
254
Structure source
AlphaFold + ColabFold
EC
3.6.1.26
GO
GO:0016020 A lipid bilayer along with all the proteins and protein complexes embedded in it and attached to it. GO:0008715 Catalysis of the reaction: CDP-diacylglycerol + H2O = a phosphatidate + CMP + 2 H+. GO:0008654 The chemical reactions and pathways resulting in the formation of a phospholipid, a lipid containing phosphoric acid as a mono- or diester. GO:0005886 The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins. GO:0046342 The chemical reactions and pathways resulting in the breakdown of CDP-diacylglycerol, CDP-1,2-diacylglycerol, a substance composed of diacylglycerol in glycosidic linkage with cytidine diphosphate.

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
CytoplasmicMembrane
ColabFold pLDDT
95.7

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 0.459
Structure A0A0H3H083
Pocket Pocket 10
P2Rank 0.333
Structure A0A0H3H083
Pocket Pocket 1
ColabFold model
FPocket 0.252 · Pocket 3
P2Rank 0.331 · Pocket 1
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 88 / 4744 genomes with a hit
Normalized 0.019

Sequence

Primary amino-acid sequence viewer.

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 5 GO

Enzyme Commission (EC)

1

Gene Ontology (GO)

5
  • GO:0016020 A lipid bilayer along with all the proteins and protein complexes embedded in it and attached to it.
  • GO:0008715 Catalysis of the reaction: CDP-diacylglycerol + H2O = a phosphatidate + CMP + 2 H+.
  • GO:0008654 The chemical reactions and pathways resulting in the formation of a phospholipid, a lipid containing phosphoric acid as a mono- or diester.
  • GO:0005886 The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.
  • GO:0046342 The chemical reactions and pathways resulting in the breakdown of CDP-diacylglycerol, CDP-1,2-diacylglycerol, a substance composed of diacylglycerol in glycosidic linkage with cytidine diphosphate.

Sequence Features

Domain/signature hits from InterPro and related databases.

19 records
Show feature table
Start End DB Term Name
1 253 PIRSF PIRSF001273 CDH
1 253 InterPro IPR003763 CDP-diacylglycerol pyrophosphatase
1 251 Hamap MF_00319 CDP-diacylglycerol pyrophosphatase [cdh].
1 251 InterPro IPR003763 CDP-diacylglycerol pyrophosphatase
26 251 Gene3D G3DSA:3.30.428.30 -
26 251 InterPro IPR036265 HIT-like superfamily
7 26 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
1 22 SignalP_EUK SignalP-TM SignalP-TM
23 254 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
1 22 Phobius SIGNAL_PEPTIDE Signal peptide region
7 17 Phobius SIGNAL_PEPTIDE_H_REGION Hydrophobic region of a signal peptide.
31 249 SUPERFAMILY SSF54197 HIT-like
31 249 InterPro IPR036265 HIT-like superfamily
18 22 Phobius SIGNAL_PEPTIDE_C_REGION C-terminal region of a signal peptide.
1 6 Phobius SIGNAL_PEPTIDE_N_REGION N-terminal region of a signal peptide.
1 250 NCBIfam TIGR00672 CDP-diacylglycerol diphosphatase
1 250 InterPro IPR015993 CDP-diacylglycerol pyrophosphatase, proteobacterial
31 249 Pfam PF02611 CDP-diacylglycerol pyrophosphatase
31 249 InterPro IPR003763 CDP-diacylglycerol pyrophosphatase

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_A0A0H3H083
AlphaFold — — full sequence — Viewing
ColabFold VK055_3461
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
10 0.459
8 0.149
13 0.098
1 0.036

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 7.52 0.333
2 1.01 0.005