Protein target profile

PA5213

glycine dehydrogenase

Genome: NC_002516.2

Gene: gcvP1 3D evidence: ColabFold model

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Length 958

Pocket druggability 0.71

Ligand records 8

EC / GO 0 / 4

Target summary

Target candidate with partial support; inspect missing evidence before prioritizing.

4 signals

How to read this page

PDB: experimentally determined structures from the Protein Data Bank. These are the strongest structural evidence, but may cover only part of the protein.

AlphaFold DB model: a precomputed predicted structure downloaded from AlphaFold Database/UniProt, not an experiment performed here.

ColabFold model: a predicted structure generated for this workspace; interpret it with coverage and confidence.

pLDDT: confidence score for predicted structures. High values support local geometry; low values mean the region should not drive pocket interpretation.

FPocket / P2Rank: software tools that predict possible ligand-binding pockets on a 3D structure. They are useful screening signals, not experimental validation.

Druggability: a pocket-based estimate of whether a small molecule could bind productively. It does not mean a drug already exists.

PDB ligand: a compound observed in an experimental structure. Direct same-protein records are stronger than homolog-transferred records.

ChEMBL: a public database of measured compound bioactivity. Direct entries are stronger than entries transferred from similar proteins.

ZINC: a purchasable-compound database. Here it marks proposed candidates from chemical similarity, not measured binders.

LigQ / LigQ_2: an internal TPW pipeline step that gathers PDB, ChEMBL, and ZINC ligand evidence for each protein.

Off-target: sequence similarity to proteins we prefer not to hit, such as human proteins or beneficial gut microbiome proteins.

DEG: Database of Essential Genes. A match suggests the protein resembles genes known to be essential in other organisms.

Roary / CoreCruncher: pan-genome tools used to decide whether a gene is core across analyzed strains or accessory/strain-specific.

EC / GO: functional annotations: EC describes enzyme reactions; GO describes biological process, molecular function, or cellular component.

KEGG pathway: a curated metabolic route label used here to group reactions imported from the metabolic model.

Chokepoint: a metabolic reaction that is the only producer or consumer of a metabolite in the imported model.

Overview

Basic information about this protein and its source genome.

Accession: PA5213
Assembly: Pseudomonas aeruginosa PAO1, complete genome
Gene: gcvP1
Status: annotated
Amino acids: 958
3D evidence: ColabFold model

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.

Target profile

Computed evidence for target prioritization.

Human off-target: Hit
Human identity (%): 65.455
Human E-value: 2.2100000000000003e-21
Gut microbiome off-target: Hit
Essential (DEG): Y
Localization: Cytoplasmic

Selected pocket evidence

The selected pocket score is the FPocket value used for ranking after applying the curated structure priority. It estimates small-molecule pocket quality; it is not experimental binding evidence. The 3D viewer may show a different loaded structure, so visible pockets can differ.

FPocket 0.71

Structure –

Pocket –

Sequence

Primary amino-acid sequence viewer.

MSQTPSLAQLQPADAFLRRHLGPDPAEQQAMLAFLGVSTRAELIVQTVPPAIRLNRPLELPAALDEQAALARLRGYAGLNQRWTSLIGMGYYGTVTPSVILRNVLENPGWYTAYTPYQPEIAQGRLEALLNFQQLTIDLTGLDLASASLLDEATAAAEAMALARRVAKARSNRFFVDAHCHPQTVSVLRTRAEAFGFELVVDEPDNLAAHAVFGALLQYPDSRGEIRDLRPLIEALHGQQALACVASDLLALLLLTPPGELGADVVLGSAQRFGVPMGYGGPHAAFFATREGYKRAMPGRIIGVSRDARGNPALRMALQTREQHIRREKANSNICTAQVLLANIASLYAVYHGPQELKRIAQRVQRLTALLAAGLKSKGLRRLNRHFFDTLTYEVGERQAAILERARAARVNLRVVDDRRLALSLDETCDAATLATLFEIFLGAGHGLDVAHLDGGAVADGIPAVLQRTSAYLQHPVFNAHHSETEMLRYLRQLEGKDLALNQAMIPLGSCTMKLNASSEMIPITWPEFAELHPFVPREQAEGYRRMIDELEAWLRAITGFDAICMQPNSGAQGEYAGLLAIRRYHQSRGDSQRDICLIPASAHGTNPASAIMASMRVVIVECDPRGNVDLDDLRLKAAEAGDRLSCLMITYPSTHGVYEEGIGEICEVVHRHGGQVYMDGANLNAQVGLARPADIGADVSHMNLHKTFCIPHGGGGPGMGPIGVKRHLAPFVANHPVIRVEGPNPLNDAVSATPWGSASILPISWMYIAMMGPQLADASEVAILSANYLANRLDGAFPVLYRGRNERVAHECILDLRPLKAQTGITEEDVAKRLMDYGFHAPTMSFPVPGTLMVEPTESESKAELDRFVEAMLSIRAEIGKVESGAWPAEDNPLKRAPHTLADVTGIWQRPYEIAEAVTPSEHARAFKYWPAVNRVDNVYGDRNLFCACVPLDDYRE

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

4 GO

Gene Ontology (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.

Sequence Features

Domain/signature hits from InterPro and related databases.

25 records

Show feature table

Start	End	DB	Term	Name
772	905	Gene3D	G3DSA:3.90.1150.10	Aspartate Aminotransferase, domain 1
772	905	InterPro	IPR015422	Pyridoxal phosphate-dependent transferase, small domain
19	950	NCBIfam	TIGR00461	aminomethyl-transferring glycine dehydrogenase
19	950	InterPro	IPR003437	Glycine dehydrogenase (decarboxylating)
484	873	CDD	cd00613	GDC-P
484	873	InterPro	IPR020581	Glycine cleavage system P protein
97	355	FunFam	G3DSA:3.40.640.10:FF:000005	Glycine dehydrogenase (decarboxylating), mitochondrial
515	771	Gene3D	G3DSA:3.40.640.10	-
515	771	InterPro	IPR015421	Pyridoxal phosphate-dependent transferase, major domain
19	442	SUPERFAMILY	SSF53383	PLP-dependent transferases
19	442	InterPro	IPR015424	Pyridoxal phosphate-dependent transferase
97	355	Gene3D	G3DSA:3.40.640.10	-
97	355	InterPro	IPR015421	Pyridoxal phosphate-dependent transferase, major domain
6	956	PANTHER	PTHR11773	GLYCINE DEHYDROGENASE, DECARBOXYLATING
6	956	InterPro	IPR020581	Glycine cleavage system P protein
767	904	FunFam	G3DSA:3.90.1150.10:FF:000007	Glycine dehydrogenase (decarboxylating), mitochondrial
473	951	SUPERFAMILY	SSF53383	PLP-dependent transferases
473	951	InterPro	IPR015424	Pyridoxal phosphate-dependent transferase
523	757	FunFam	G3DSA:3.40.640.10:FF:000007	glycine dehydrogenase (Decarboxylating), mitochondrial
18	441	Pfam	PF02347	Glycine cleavage system P-protein
18	441	InterPro	IPR020581	Glycine cleavage system P protein
66	441	CDD	cd00613	GDC-P
66	441	InterPro	IPR020581	Glycine cleavage system P protein
10	956	Hamap	MF_00711	Glycine dehydrogenase (decarboxylating) [gcvP].
10	956	InterPro	IPR003437	Glycine dehydrogenase (decarboxylating)

3D Structure

Selected loaded structure. Experimental PDB entries may cover only a portion of the sequence; AlphaFold DB and ColabFold models typically cover the full protein but remain computational predictions.

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Structural evidence

0 + 1

Experimental PDB entries plus predicted AlphaFold DB or ColabFold models. Click Switch to display a different loaded structure in the viewer.

Entry	Method	Resolution	Chain	Coverage	Links	Status
ColabFold PA5213	ColabFold	—	—	full sequence	—	Viewing

Pocket details Inspect a specific pocket, or open the full viewer

Binding pockets · FPocket

Druggability: high ≥ 0.7 · medium 0.4–0.69 · low < 0.4

Site 1 FPocket #9

0.71

Show in viewer

Site 2 FPocket #1

0.304

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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

Chemistry signal

Structural ligand evidence is available for this target.

Direct evidence 0 8 via homologs

Structural ligands 2 0 loaded crystals

Bioactive compounds 0 6 ZINC proposed compounds

Drug-like & clean 8 0 PAINS alerts

Best available ligand signal

AOA PDB via homolog 91.1 Da · LogP -1.04 · TPSA 72.5 Open detail RCSB PDB

Detail RCSB PDB AOA PDB via homolog

Detail RCSB PDB PLG PDB via homolog

Detail ZINC ZINC1532708 ZINC proposed compound · Tanimoto 0.674

Detail ZINC ZINC1532705 ZINC proposed compound · Tanimoto 0.652

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.

No PDB structure with a co-crystallized ligand found for this exact protein.

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.

Ligand	Source crystal	UniProt (homolog)	MW · LogP · TPSA	Lipinski	PAINS	SMILES
AOA RCSB PDB	1WYV	Q5SKW7	91.1 Da LogP -1.04 TPSA 72.5	✓ Ro5	✓ Clean	`C(C(=O)O)ON`
PLG RCSB PDB	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`

Experimental bioactivity from ChEMBL measured directly on this protein. Score = pchembl (−log Ki/IC₅₀; higher = more potent).

No ChEMBL bioactivity data found for this exact protein.

Bioactivity inferred from similar proteins in ChEMBL. Score = pchembl (−log Ki/IC₅₀; higher = more potent).

No ChEMBL hits found through similar proteins.

Proposed virtual-screening candidates from ZINC. Score = Tanimoto similarity to a known binder (0–1; higher = more similar).

Ligand	Tanimoto	MW · LogP · TPSA	Lipinski	PAINS	SMILES
ZINC1532708 ZINC	0.674	248.2 Da LogP 0.16 TPSA 125.9	✓ Ro5	✓ Clean	`Cc1ncc(COP(=O)(O)O)c(CN)c1O`
ZINC1532705 ZINC	0.652	249.2 Da LogP 0.20 TPSA 120.1	✓ Ro5	✓ Clean	`Cc1ncc(COP(=O)(O)O)c(CO)c1O`
ZINC1656021 ZINC	0.587	233.2 Da LogP 1.01 TPSA 99.9	✓ Ro5	✓ Clean	`Cc1ncc(COP(=O)(O)O)c(C)c1O`
ZINC1532514 ZINC	0.583	247.1 Da LogP 0.52 TPSA 117.0	✓ Ro5	✓ Clean	`Cc1ncc(COP(=O)(O)O)c(C=O)c1O`
ZINC2114966 ZINC	0.534	332.2 Da LogP 0.99 TPSA 149.5	✓ Ro5	✓ Clean	`Cc1ncc(COP(=O)(O)O)c(/C=N/CCCC(=O)O)c1O`
ZINC59703646 ZINC	0.500	234.2 Da LogP -0.98 TPSA 127.2	✓ Ro5	✓ Clean	`O=C(O)COC(=O)CCC(=O)OCC(=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.