Protein target profile

KP13_02169

D-3-phosphoglycerate dehydrogenase

Genome: KpKP13 Gene: AHE42739.1 serA 3D evidence: AlphaFold DB model + ColabFold model UniProt A0A0H3GSY5
Length 410
Pocket druggability 0.079
Direct ligand evidence 0 170 total records
Functional annotation 2 EC 6 GO
Target summary

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

Automated synthesis of the evidence currently loaded. Review the underlying records before prioritizing this protein.

Terms and data sources used on 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 Target 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.

Prioritization evidence

Selectivity, essentiality, structural confidence, conservation, and predicted binding-site evidence.

Off-target risk

Human off-target
Hit
Human identity (%)
41.27 Lower values reduce human off-target concern.
Human E-value
9.22e-06
Gut microbiome similarity
4.7% of screened genomes Lower prevalence suggests narrower overlap with the screened gut microbiome.

Essentiality

Essential (DEG)
Y
DEG identity (%)
70.905 Higher values support similarity to known essential genes.
DEG E-value
0.0 Smaller values mean stronger essential-gene similarity.

Localization

Localization
Cytoplasmic

Structure confidence

ColabFold pLDDT
95.72 0-100 confidence; >70 supports local structural interpretation.

Binding-site evidence

AlphaFold DB / UniProt model

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 0.079
Structure A0A0H3GSY5
Pocket Pocket 14
P2Rank 0.916
Structure A0A0H3GSY5
Pocket Pocket 1
ColabFold model
FPocket 0.275 · Pocket 17
P2Rank 0.861 · Pocket 1
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 222 / 4744 genomes with a hit
Prevalence 4.7%

Cross-references

External database identifiers for this protein, its structures, ligands, and metabolic reactions.

Chemistry

ChEMBL CHEMBL4541133 ChEMBL CHEMBL4536737 ChEMBL CHEMBL4584313 ChEMBL CHEMBL4436264 ChEMBL CHEMBL4518579 ChEMBL CHEMBL4467246 ChEMBL CHEMBL4515492 ChEMBL CHEMBL4527607 ChEMBL CHEMBL4579388 ChEMBL CHEMBL4540875 ChEMBL CHEMBL4521661 ChEMBL CHEMBL4542437 ChEMBL CHEMBL4483622 ChEMBL CHEMBL4541457 ChEMBL CHEMBL4548014 ChEMBL CHEMBL4587306 ChEMBL CHEMBL4483483 ChEMBL CHEMBL4533417 ChEMBL CHEMBL4547034 ChEMBL CHEMBL4526788 ChEMBL CHEMBL4548203 ChEMBL CHEMBL4560976 ChEMBL CHEMBL4522256 ChEMBL CHEMBL4517873 ChEMBL CHEMBL4536020 ChEMBL CHEMBL4580665 ChEMBL CHEMBL4585012 ChEMBL CHEMBL4545772 ChEMBL CHEMBL4518612 ChEMBL CHEMBL4513843 ChEMBL CHEMBL4522032 ChEMBL CHEMBL4536556 ChEMBL CHEMBL4592933 ChEMBL CHEMBL4517506 ChEMBL CHEMBL4547905 ChEMBL CHEMBL4548756 ChEMBL CHEMBL4572814 ChEMBL CHEMBL4542730 ChEMBL CHEMBL4572184 ChEMBL CHEMBL4438014 ChEMBL CHEMBL4557404 ChEMBL CHEMBL4443265 ChEMBL CHEMBL4587964 ChEMBL CHEMBL4536870 ChEMBL CHEMBL4551822 ChEMBL CHEMBL4582792 ChEMBL CHEMBL4524231 ChEMBL CHEMBL4591375 ChEMBL CHEMBL4550162 ChEMBL CHEMBL4514445 ChEMBL CHEMBL4531113 ChEMBL CHEMBL4556963 ChEMBL CHEMBL4458393 ChEMBL CHEMBL4476654 ChEMBL CHEMBL4541970 ChEMBL CHEMBL4522467 ChEMBL CHEMBL4594097 ChEMBL CHEMBL4576106 ChEMBL CHEMBL4522081 ChEMBL CHEMBL4469992 ChEMBL CHEMBL4473052 ChEMBL CHEMBL4534115 ChEMBL CHEMBL4578644 ChEMBL CHEMBL4577108 ChEMBL CHEMBL4545321 ChEMBL CHEMBL4452531 ChEMBL CHEMBL4535665 ChEMBL CHEMBL4580853 ChEMBL CHEMBL4590502 ChEMBL CHEMBL4455598 ChEMBL CHEMBL4513944 ChEMBL CHEMBL4549808 ChEMBL CHEMBL4557402 ChEMBL CHEMBL4565578 ChEMBL CHEMBL4474620 ChEMBL CHEMBL4563552 ChEMBL CHEMBL4521930 ChEMBL CHEMBL4552712 ChEMBL CHEMBL4580038 ChEMBL CHEMBL4574871 ChEMBL CHEMBL4579433 ChEMBL CHEMBL4457646 ChEMBL CHEMBL4516261 ChEMBL CHEMBL4535659 ChEMBL CHEMBL4560125 ChEMBL CHEMBL4569609 ChEMBL CHEMBL4578446 ChEMBL CHEMBL4530135 ChEMBL CHEMBL4573469 ChEMBL CHEMBL4518189 ChEMBL CHEMBL4565713 ChEMBL CHEMBL4571043 ChEMBL CHEMBL4549376 ChEMBL CHEMBL4437057 ChEMBL CHEMBL4550369 ChEMBL CHEMBL4593777 ChEMBL CHEMBL4568292 ChEMBL CHEMBL4590594 ChEMBL CHEMBL4530767 ChEMBL CHEMBL4548661

Sequence

Primary amino-acid sequence viewer.

MAKVSLEKDKIKFLLVEGVHQKAIDSLRAAGYTNIEFHKGALDSEQLKASIRDAHFIGLRSRTHLTEEIFAAAEKLVAVGCFCIGTNQVDLNAAAKRGIPVFNAPFSNTRSVAELVIGELLLMLRGVPEANAKAHRGVWNKQAVGSFEARGKKLGIIGYGHIGTQLGILAESLGMHVFFYDIENKLPLGNATQVQHLSDLLNMSDVVSLHVPENASTKNMMGAEELALMKPGALLINASRGTVVDIPALCDALASKHLAGAAIDVFPTEPATNSDPFTSPLCEFDNVILTPHIGGSTQEAQENIGLEVAGKLAKYSDNGSTLSAVNFPEVSLPLHGGRRLLHIHENRPGVLTAINQIFAAQSINIAAQYLQTSPQMGYVVIDIEAEEDVAQQALQAMKAIPGTIRARLLF

Functional annotations

Enzyme classification and Gene Ontology terms linked to this protein.

2 EC 6 GO

Enzyme Commission (EC)

2

Gene Ontology (GO)

6
  • GO:0051287 Binding to nicotinamide adenine dinucleotide, a coenzyme involved in many redox and biosynthetic reactions; binding may be to either the oxidized form, NAD+, or the reduced form, NADH.
  • GO:0016616 Catalysis of an oxidation-reduction (redox) reaction in which a CH-OH group acts as a hydrogen or electron donor and reduces NAD+ or NADP.
  • GO:0005829 The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
  • GO:0047545 Catalysis of the reaction: (S)-2-hydroxyglutarate + acceptor = 2-oxoglutarate + reduced acceptor.
  • GO:0004617 Catalysis of the reaction: 3-phosphoglycerate + NAD+ = 3-phosphohydroxypyruvate + NADH + H+.
  • GO:0006564 The chemical reactions and pathways resulting in the formation of L-serine.

Sequence domains and features

Domain and signature matches imported from InterPro and related databases.

25 records
Show feature table
Start End DB Term Name
14 312 Gene3D G3DSA:3.40.50.720 -
119 294 Pfam PF02826 D-isomer specific 2-hydroxyacid dehydrogenase, NAD binding domain
119 294 InterPro IPR006140 D-isomer specific 2-hydroxyacid dehydrogenase, NAD-binding domain
339 410 ProSiteProfiles PS51671 ACT domain profile.
339 410 InterPro IPR002912 ACT domain
154 181 ProSitePatterns PS00065 D-isomer specific 2-hydroxyacid dehydrogenases NAD-binding signature.
154 181 InterPro IPR029752 D-isomer specific 2-hydroxyacid dehydrogenase, NAD-binding domain conserved site 1
109 297 Gene3D G3DSA:3.40.50.720 -
229 245 ProSitePatterns PS00671 D-isomer specific 2-hydroxyacid dehydrogenases signature 3.
229 245 InterPro IPR029753 D-isomer specific 2-hydroxyacid dehydrogenase, NAD-binding domain conserved site
339 409 CDD cd04901 ACT_3PGDH
200 222 ProSitePatterns PS00670 D-isomer specific 2-hydroxyacid dehydrogenases signature 2.
200 222 InterPro IPR029753 D-isomer specific 2-hydroxyacid dehydrogenase, NAD-binding domain conserved site
7 138 SUPERFAMILY SSF52283 Formate/glycerate dehydrogenase catalytic domain-like
328 409 SUPERFAMILY SSF55021 ACT-like
328 409 InterPro IPR045865 ACT-like domain
108 295 SUPERFAMILY SSF51735 NAD(P)-binding Rossmann-fold domains
108 295 InterPro IPR036291 NAD(P)-binding domain superfamily
328 409 FunFam G3DSA:3.30.70.260:FF:000007 D-3-phosphoglycerate dehydrogenase
11 315 CDD cd12176 PGDH_3
14 326 Pfam PF00389 D-isomer specific 2-hydroxyacid dehydrogenase, catalytic domain
14 326 InterPro IPR006139 D-isomer specific 2-hydroxyacid dehydrogenase, catalytic domain
328 409 Gene3D G3DSA:3.30.70.260 -
109 297 FunFam G3DSA:3.40.50.720:FF:000041 D-3-phosphoglycerate dehydrogenase
43 322 PANTHER PTHR10996 2-HYDROXYACID DEHYDROGENASE-RELATED

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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Pocket score High Medium Low
How colors and pocket overlays are used
Uniform protein color marks the displayed model as a single molecular object.
Experimental PDB structures may be colored by chain to distinguish subunits or copies present in the file.
Pocket colors and alpha spheres are evidence overlays for predicted binding cavities; they are not alternative protein chains.
'Alpha spheres' is FPocket's own cavity-shape geometry, imported when available and aligned with the loaded structure.
'Pocket atoms'/'Predicted site atoms' show the pocket's residue atoms instead: P2Rank reports residues rather than alpha spheres, and FPocket falls back to this when alpha-sphere geometry is unavailable or doesn't align.
'No pocket geometry' means neither alpha spheres nor residue-position data could be found for that pocket; the layer just highlights the same residues as 'Nearby residues'.
Pocket details Inspect a specific pocket, or open the full viewer

Binding pockets · P2Rank

Probability: high ≥ 0.5 · medium 0.2–0.49 · low < 0.2

Site 1 P2Rank #1
0.916
Show in viewer
Surrounding area
Site 2 P2Rank #2
0.166
Show in viewer
Surrounding area
Site 3 P2Rank #3
0.156
Show in viewer
Surrounding area
All structural evidence 0 experimental · 2 predicted

Structural evidence

0 + 2

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
AlphaFold DB AF_A0A0H3GSY5
AlphaFold DB full sequence Viewing
ColabFold KP13_02169
ColabFold full sequence Loaded

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.

170 records
Chemistry signal

Structural and bioactivity evidence are both available for this target.

Direct evidence 0 same-protein records
Transferred evidence 120 records from similar proteins
Structural ligands 20 0 loaded crystals
Measured bioactivity 100 direct and transferred ChEMBL records
Proposed compounds 50 similarity-based ZINC candidates
Best available ligand signal
3PG PDB via homolog 186.1 Da · LogP -1.46 · TPSA 124.3 Open detail RCSB PDB
5AO PDB via homolog Detail RCSB PDB
8NB PDB via homolog Detail RCSB PDB
9EW PDB via homolog Detail RCSB PDB
9EZ PDB via homolog Detail RCSB PDB

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
3PG RCSB PDB O43175 186.1 Da LogP -1.46 TPSA 124.3 ✓ Ro5 ✓ Clean C([C@H](C(=O)O)O)OP(=O)(O)O
5AO RCSB PDB O43175 160.2 Da LogP 1.92 TPSA 52.0 ✓ Ro5 ✓ Clean c1cc(cc(c1)N)c2cnco2
8NB RCSB PDB O43175 199.6 Da LogP 2.31 TPSA 38.3 ✓ Ro5 ✓ Clean CC(=O)Nc1ccc(c(c1)Cl)OC
9EW RCSB PDB O43175 135.1 Da LogP 1.53 TPSA 46.3 ✓ Ro5 ✓ Clean c1ccc2c(c1)c(no2)O
9EZ RCSB PDB O43175 173.2 Da LogP 1.67 TPSA 43.8 ✓ Ro5 ✓ Clean Cn1c(cc(n1)c2ccccc2)N
9TT RCSB PDB O43175 146.2 Da LogP 1.76 TPSA 30.9 ✓ Ro5 Alert Cn1ccc2c1ccc(c2)N
9TW RCSB PDB O43175 173.6 Da LogP 1.58 TPSA 43.1 ✓ Ro5 ✓ Clean c1cc(c(cc1C(=O)N)Cl)F
9TZ RCSB PDB O43175 154.1 Da LogP 1.83 TPSA 37.3 ✓ Ro5 ✓ Clean Cc1ccc(cc1C(=O)O)F
AKG RCSB PDB P0A9T0 146.1 Da LogP -0.50 TPSA 91.7 ✓ Ro5 ✓ Clean C(CC(=O)O)C(=O)C(=O)O
GLV RCSB PDB Q8U3Y2 74.0 Da LogP -0.73 TPSA 54.4 ✓ Ro5 ✓ Clean C(=O)C(=O)O
HMT RCSB PDB O43175 545.6 Da LogP 2.58 TPSA 124.0 1 viol. ✓ Clean CC(C)(CCC[C@@](CC(=O)OC)(C(=O)O[C@H]1[C@H]2c3cc…
HPV RCSB PDB P9WNX3 184.0 Da LogP -1.25 TPSA 121.1 ✓ Ro5 ✓ Clean C(C(=O)C(=O)O)OP(=O)(O)O
K4T RCSB PDB O43175 241.3 Da LogP 1.98 TPSA 46.9 ✓ Ro5 ✓ Clean Cn1c(cc(n1)c2ccccc2)C(=O)NC3CC3
K5K RCSB PDB O43175 499.4 Da LogP 3.12 TPSA 125.7 ✓ Ro5 ✓ Clean Cc1cc2c(cc(n2C)C(=O)N[C@H](CO)c3ccc(cc3)S(=O)(=…
LAC RCSB PDB O66939 90.1 Da LogP -0.55 TPSA 57.5 ✓ Ro5 ✓ Clean C[C@H](C(=O)O)O
MLI RCSB PDB F8AEA4 102.0 Da LogP -3.12 TPSA 80.3 ✓ Ro5 ✓ Clean C(C(=O)[O-])C(=O)[O-]
MLT RCSB PDB O43175 134.1 Da LogP -1.09 TPSA 94.8 ✓ Ro5 ✓ Clean C([C@H](C(=O)O)O)C(=O)O
ONS RCSB PDB O43175 510.4 Da LogP 4.75 TPSA 93.5 1 viol. ✓ Clean Cn1c2ccc(c(c2cc1C(=O)NC3(COC3)c4ccc(cc4)[C@@H](…
PPI RCSB PDB O66939 74.1 Da LogP 0.48 TPSA 37.3 ✓ Ro5 ✓ Clean CCC(=O)O
TLA RCSB PDB O43175 150.1 Da LogP -2.12 TPSA 115.1 ✓ Ro5 ✓ Clean [C@@H]([C@H](C(=O)O)O)(C(=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.