Protein profile

VK055_4144

glycine dehydrogenase

Genome: KpATCC43816

Gene: gcvP AIK82690.1 Structure source: AlphaFold + ColabFold UniProt A0A0H3GXC7
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Amino acids 957
Annotations 10
Features 27
PDB binders 2
Druggability 0.961

Overview

Basic information about this protein and its source genome.

Accession
VK055_4144
Assembly
Klebsiella pneumoniae subsp. pneumoniae strain ATCC 43816 KPPR1, complete genome
Gene
gcvP AIK82690.1
Status
annotated
Amino acids
957
Structure source
AlphaFold + ColabFold
EC
1.4.4.2
GO
GO:0006546 The chemical reactions and pathways resulting in the breakdown of glycine. 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:0006544 The chemical reactions and pathways involving glycine, aminoethanoic acid. GO:0004375 Catalysis of the reaction: N(6)-[(R)-lipoyl]-L-lysyl-[glycine-cleavage complex H protein] + glycine + H+ = N(6)-[(R)-S(8)-aminomethyldihydrolipoyl]-L-lysyl-[glycine-cleavage complex H protein] + CO2. GO:0005829 The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes. GO:0005960 A protein complex that catalyzes the reversible oxidation of glycine. In E. coli, it has four components: dihydrolipoamide dehydrogenase, glycine dehydrogenase (decarboxylating), lipoyl-GcvH-protein and aminomethyltransferase, also known as L, P, H, and T.

Target profile

Computed evidence for target prioritization.

Human off-target
hit
Human identity (%)
67.273
Human E-value
2.72e-20
Gut microbiome off-target
hit
Essential (DEG)
Y
DEG identity (%)
55.14
DEG E-value
0.0
Localization
Cytoplasmic
ColabFold pLDDT
95.97

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 0.961
Structure A0A0H3GXC7
Pocket Pocket 3
P2Rank 0.953
Structure A0A0H3GXC7
Pocket Pocket 1
ColabFold model
FPocket 0.921 · Pocket 2
P2Rank 0.974 · Pocket 1
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 405 / 4744 genomes with a hit
Normalized 0.085

Sequence

Primary amino-acid sequence viewer.

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 9 GO

Enzyme Commission (EC)

1

Gene Ontology (GO)

9
  • GO:0006546 The chemical reactions and pathways resulting in the breakdown of glycine.
  • 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:0006544 The chemical reactions and pathways involving glycine, aminoethanoic acid.
  • GO:0004375 Catalysis of the reaction: N(6)-[(R)-lipoyl]-L-lysyl-[glycine-cleavage complex H protein] + glycine + H+ = N(6)-[(R)-S(8)-aminomethyldihydrolipoyl]-L-lysyl-[glycine-cleavage complex H protein] + CO2.
  • GO:0005829 The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
  • GO:0005960 A protein complex that catalyzes the reversible oxidation of glycine. In E. coli, it has four components: dihydrolipoamide dehydrogenase, glycine dehydrogenase (decarboxylating), lipoyl-GcvH-protein and aminomethyltransferase, also known as L, P, H, and T.
  • GO:0016594 Binding to glycine, aminoethanoic acid.
  • GO:0030170 Binding to pyridoxal 5' phosphate, 3-hydroxy-5-(hydroxymethyl)-2-methyl4-pyridine carboxaldehyde 5' phosphate, the biologically active form of vitamin B6.
  • GO:0019464 The chemical reactions and pathways resulting in the breakdown of glycine by oxidative cleavage to carbon dioxide, ammonia, and a methylene group, mediated by enzymes of the glycine cleavage complex.

Sequence Features

Domain/signature hits from InterPro and related databases.

27 records
Show feature table
Start End DB Term Name
8 956 Hamap MF_00711 Glycine dehydrogenase (decarboxylating) [gcvP].
8 956 InterPro IPR003437 Glycine dehydrogenase (decarboxylating)
17 950 NCBIfam TIGR00461 aminomethyl-transferring glycine dehydrogenase
17 950 InterPro IPR003437 Glycine dehydrogenase (decarboxylating)
485 875 CDD cd00613 GDC-P
485 875 InterPro IPR020581 Glycine cleavage system P protein
4 956 PANTHER PTHR11773 GLYCINE DEHYDROGENASE, DECARBOXYLATING
4 956 InterPro IPR020581 Glycine cleavage system P protein
95 355 FunFam G3DSA:3.40.640.10:FF:000005 Glycine dehydrogenase (decarboxylating), mitochondrial
17 440 SUPERFAMILY SSF53383 PLP-dependent transferases
17 440 InterPro IPR015424 Pyridoxal phosphate-dependent transferase
64 439 CDD cd00613 GDC-P
64 439 InterPro IPR020581 Glycine cleavage system P protein
463 951 SUPERFAMILY SSF53383 PLP-dependent transferases
463 951 InterPro IPR015424 Pyridoxal phosphate-dependent transferase
524 771 Gene3D G3DSA:3.40.640.10 -
524 771 InterPro IPR015421 Pyridoxal phosphate-dependent transferase, major domain
96 355 Gene3D G3DSA:3.40.640.10 -
96 355 InterPro IPR015421 Pyridoxal phosphate-dependent transferase, major domain
16 438 Pfam PF02347 Glycine cleavage system P-protein
16 438 InterPro IPR020581 Glycine cleavage system P protein
461 739 Pfam PF02347 Glycine cleavage system P-protein
461 739 InterPro IPR020581 Glycine cleavage system P protein
772 905 Gene3D G3DSA:3.90.1150.10 Aspartate Aminotransferase, domain 1
772 905 InterPro IPR015422 Pyridoxal phosphate-dependent transferase, small domain
524 758 FunFam G3DSA:3.40.640.10:FF:000007 glycine dehydrogenase (Decarboxylating), mitochondrial
768 906 FunFam G3DSA:3.90.1150.10:FF:000007 Glycine dehydrogenase (decarboxylating), mitochondrial

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_A0A0H3GXC7
AlphaFold — — full sequence — Viewing
ColabFold VK055_4144
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
3 0.961
6 0.381

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 31.06 0.937
2 7.74 0.409
3 4.12 0.166
4 2.22 0.054
5 1.69 0.029

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.

8 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
AOA
1WYV
Q5SKW7 91.1 Da LogP -1.04 TPSA 72.5 ✓ Ro5 ✓ Clean C(C(=O)O)ON
PLG
6I35
P23378 306.2 Da LogP -0.12 TPSA 149.2 ✓ Ro5 ✓ Clean Cc1c(c(c(cn1)COP(=O)(O)O)CNCC(=O)O)O

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.