KpKP13 Protein target profile

Dihydrofolate reductase

Accession: KP13_01960

Gene: folA AHE46399.1 3D evidence: AlphaFold DB model + ColabFold model UniProt A0A0H3GI29
Length 159
Pocket druggability (P2Rank · AlphaFold DB model) 0.936
Direct ligand evidence 0 184 total records
Functional annotation 1 EC 9 GO
Target summary

Promising target candidate with multiple supporting evidence streams.

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 (%)
27.473 Lower values reduce human off-target concern.
Human E-value
1.86e-11
Gut microbiome similarity
3.1% of screened genomes Lower prevalence suggests narrower overlap with the screened gut microbiome.

Essentiality

Essential (DEG)
Y
DEG identity (%)
94.969 Higher values support similarity to known essential genes.
DEG E-value
1.55e-113 Smaller values mean stronger essential-gene similarity.

Structure confidence

ColabFold pLDDT
96.06 0-100 confidence; >70 supports local structural interpretation.

Binding-site evidence

AlphaFold DB / UniProt model

P2Rank's binding-site probability is the primary druggability signal shown across the app; FPocket's druggability score is shown alongside it for comparison. Both estimate small-molecule pocket quality after applying the curated structure priority — neither is experimental binding evidence. The 3D viewer may show a different loaded structure, so visible pockets can differ.

Druggability (P2Rank) 0.936
Structure A0A0H3GI29
Pocket Pocket 1
Druggability (FPocket) 0.615
Structure A0A0H3GI29
Pocket Pocket 1
ColabFold model
P2Rank 0.904 · Pocket 1
FPocket 0.419 · Pocket 6
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 149 / 4744 genomes with a hit
Prevalence 3.1%

Sequence

Primary amino-acid sequence viewer.

MISLIAALAVDRVIGMENAMPWNLPADLAWFKRNTLNKPVVMGRLTWESIGRPLPGRKNIVISSKPGSDDRVQWVSSVEEAIAACGDVEEIMVIGGGRVYEQFLPKAQKLYLTHIDAEVEGDTHFPDYDPDEWESVFSEFHDADAQNSHSYCFEILERR

Functional annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 9 GO

Subcellular localization

Localization
Cytoplasmic

Enzyme Commission (EC)

1

Gene Ontology (GO)

9
  • GO:0050661 Binding to nicotinamide-adenine dinucleotide phosphate, a coenzyme involved in many redox and biosynthetic reactions; binding may be to either the oxidized form, NADP+, or the reduced form, NADPH.
  • GO:0004146 Catalysis of the reaction: 5,6,7,8-tetrahydrofolate + NADP+ = 7,8-dihydrofolate + NADPH + H+.
  • GO:0046654 The chemical reactions and pathways resulting in the formation of tetrahydrofolate, 5,6,7,8-tetrahydrofolic acid, a folate derivative bearing additional hydrogens on the pterin group.
  • GO:0006545 The chemical reactions and pathways resulting in the formation of glycine, aminoethanoic acid.
  • GO:0005829 The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
  • GO:0070401 Binding to the oxidized form, NADP+, of nicotinamide-adenine dinucleotide phosphate, a coenzyme involved in many redox and biosynthetic reactions.
  • GO:0046452 The chemical reactions and pathways involving dihydrofolate, the dihydroxylated derivative of folate.
  • GO:0046655 The chemical reactions and pathways involving folic acid, pteroylglutamic acid. Folic acid is widely distributed as a member of the vitamin B complex and is essential for the synthesis of purine and pyrimidines.
  • GO:0006730 The chemical reactions and pathways involving the transfer of one-carbon units in various oxidation states.

Sequence domains and features

Domain and signature matches imported from InterPro and related databases.

24 records
Show feature table
Start End DB Term Name
1 15 Phobius SIGNAL_PEPTIDE Signal peptide region
13 35 ProSitePatterns PS00075 Dihydrofolate reductase (DHFR) domain signature.
13 35 InterPro IPR017925 Dihydrofolate reductase conserved site
2 157 CDD cd00209 DHFR
2 157 InterPro IPR001796 Dihydrofolate reductase domain
16 159 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
1 158 Pfam PF00186 Dihydrofolate reductase
1 158 InterPro IPR001796 Dihydrofolate reductase domain
2 10 Phobius SIGNAL_PEPTIDE_H_REGION Hydrophobic region of a signal peptide.
1 158 ProSiteProfiles PS51330 Dihydrofolate reductase (DHFR) domain profile.
1 159 Gene3D G3DSA:3.40.430.10 Dihydrofolate Reductase, subunit A
1 159 InterPro IPR024072 Dihydrofolate reductase-like domain superfamily
2 157 PANTHER PTHR48069 DIHYDROFOLATE REDUCTASE
2 157 InterPro IPR012259 Dihydrofolate reductase
1 1 Phobius SIGNAL_PEPTIDE_N_REGION N-terminal region of a signal peptide.
11 15 Phobius SIGNAL_PEPTIDE_C_REGION C-terminal region of a signal peptide.
1 159 FunFam G3DSA:3.40.430.10:FF:000001 Dihydrofolate reductase
1 159 PIRSF PIRSF000194 DHFR
1 159 InterPro IPR012259 Dihydrofolate reductase
1 159 SUPERFAMILY SSF53597 Dihydrofolate reductase-like
27 35 PRINTS PR00070 Dihydrofolate reductase signature
40 51 PRINTS PR00070 Dihydrofolate reductase signature
90 104 PRINTS PR00070 Dihydrofolate reductase signature
13 23 PRINTS PR00070 Dihydrofolate reductase signature

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

Druggability (P2Rank): high ≥ 0.5 · medium 0.2–0.49 · low < 0.2

Pocket 1 P2Rank #1
0.936
Likely same site as FPocket 1 0.7 Å 29 shared residues 97% of smaller site
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Surrounding area
Pocket 2 P2Rank #2
0.035
Show in viewer
Surrounding area
Pocket 3 P2Rank #3
0.011
Show in viewer
Surrounding area

Binding pockets · FPocket

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

Pocket 1 FPocket #1
0.615 Unusual size
Likely same site as P2Rank 1 0.7 Å 29 shared residues 97% of smaller site
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_A0A0H3GI29
AlphaFold DB full sequence Viewing
ColabFold KP13_01960
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.

184 records
Chemistry signal

Structural and bioactivity evidence are both available for this target.

Direct evidence 0 same-protein records
Transferred evidence 134 records from similar proteins
Structural ligands 34 0 loaded crystals
Measured bioactivity 100 direct and transferred ChEMBL records
Proposed compounds 50 similarity-based ZINC candidates
Best available ligand signal
2MX PDB via homolog 1031.2 Da · LogP 2.34 · TPSA 404.7 Open detail RCSB PDB
31I PDB via homolog Detail RCSB PDB
34R PDB via homolog Detail RCSB PDB
34S PDB via homolog Detail RCSB PDB
35I 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
2MX RCSB PDB P0ABQ4 1031.2 Da LogP 2.34 TPSA 404.7 3 viol. ✓ Clean CN(Cc1cnc2c(n1)c(nc(n2)N)N)c3ccc(cc3)C(=O)N[C@@…
31I RCSB PDB Q81R22 486.6 Da LogP 3.84 TPSA 129.0 ✓ Ro5 ✓ Clean CC(C)[C@H]1c2ccccc2C=NN1C(=O)/C=C/c3cc(cc(c3OC)…
34R RCSB PDB Q81R22 520.6 Da LogP 4.23 TPSA 129.0 1 viol. ✓ Clean COc1cc(cc(c1OC)/C=C/C(=O)N2[C@@H](c3ccccc3C=N2)…
34S RCSB PDB Q81R22 520.6 Da LogP 4.23 TPSA 129.0 1 viol. ✓ Clean COc1cc(cc(c1OC)/C=C/C(=O)N2[C@H](c3ccccc3C=N2)c…
35I RCSB PDB Q81R22 540.5 Da LogP 4.52 TPSA 129.0 1 viol. ✓ Clean COc1cc(cc(c1OC)/C=C/C(=O)N2[C@H](c3ccccc3C=N2)C…
52I RCSB PDB Q81R22 500.6 Da LogP 4.23 TPSA 129.0 1 viol. ✓ Clean CC(C)C[C@@H]1c2ccccc2C=NN1C(=O)/C=C/c3cc(cc(c3O…
52J RCSB PDB Q81R22 500.6 Da LogP 4.23 TPSA 129.0 1 viol. ✓ Clean CC(C)C[C@H]1c2ccccc2C=NN1C(=O)/C=C/c3cc(cc(c3OC…
53I RCSB PDB Q81R22 498.6 Da LogP 4.15 TPSA 129.0 ✓ Ro5 ✓ Clean CC(=C[C@@H]1c2ccccc2C=NN1C(=O)/C=C/c3cc(cc(c3OC…
53J RCSB PDB Q81R22 498.6 Da LogP 4.15 TPSA 129.0 ✓ Ro5 ✓ Clean CC(=C[C@H]1c2ccccc2C=NN1C(=O)/C=C/c3cc(cc(c3OC)…
5WB RCSB PDB Q81R22 358.4 Da LogP 1.71 TPSA 114.7 ✓ Ro5 ✓ Clean Cc1c(c(nc(n1)N)N)C#CC(c2cc(c(c(c2)OC)OC)OC)OC
6ME RCSB PDB P0ABQ4 178.2 Da LogP 0.77 TPSA 77.8 ✓ Ro5 ✓ Clean C[C@H]1CCc2c(c(nc(n2)N)N)C1
7ME RCSB PDB P0ABQ4 178.2 Da LogP 0.77 TPSA 77.8 ✓ Ro5 ✓ Clean C[C@H]1CCc2c(nc(nc2N)N)C1
817 RCSB PDB P0ABQ4 276.3 Da LogP 2.36 TPSA 85.8 ✓ Ro5 ✓ Clean [H]/N=C(\N)/N/C(=N/[H])/SCc1cccc(c1)C(F)(F)F
8CV RCSB PDB P0ABQ4 205.3 Da LogP 0.24 TPSA 97.8 ✓ Ro5 ✓ Clean [H]/N=C(/N)\N/C(=N/[H])/NCCc1ccccc1
8DM RCSB PDB P0ABQ4 266.3 Da LogP 0.32 TPSA 129.7 ✓ Ro5 ✓ Clean c1cc(ccc1C(=O)N[C@@H](CCC(=O)O)C(=O)O)N
ATR RCSB PDB P0ABQ4 507.2 Da LogP -1.63 TPSA 279.1 3 viol. ✓ Clean c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)…
BFR RCSB PDB P0ABQ4 157.2 Da LogP -0.42 TPSA 100.3 ✓ Ro5 ✓ Clean [H]/N=C(\NCCCC)/N=C(N)N
C1A RCSB PDB P0ABQ4 366.5 Da LogP 1.61 TPSA 171.5 1 viol. ✓ Clean [H]/N=C(/N/C(=N\[H])/SCc1c(cc(c(c1)C)CS/C(=N/[H…
DDF RCSB PDB P0ABQ4 443.5 Da LogP 0.62 TPSA 187.5 1 viol. ✓ Clean c1cc(ccc1CC[C@@H]2CC3=C(NC2)NC(=NC3=O)N)C(=O)N[…
DHF RCSB PDB P0ABQ4 443.4 Da LogP 0.01 TPSA 211.9 1 viol. ✓ Clean c1cc(ccc1C(=O)N[C@@H](CCC(=O)O)C(=O)O)NCC2=NC3=…
DZF RCSB PDB P0ABQ4 440.4 Da LogP 0.56 TPSA 200.4 1 viol. ✓ Clean c1cc(ccc1C(=O)N[C@@H](CCC(=O)O)C(=O)O)NCc2cc3c(…
FFO RCSB PDB P0ABQ4 473.4 Da LogP -0.73 TPSA 219.8 1 viol. ✓ Clean c1cc(ccc1C(=O)NC(CCC(=O)O)C(=O)O)NCC2CNC3=C(N2C…
FOL RCSB PDB Q1RGF0 441.4 Da LogP -0.04 TPSA 213.3 1 viol. ✓ Clean c1cc(ccc1C(=O)N[C@@H](CCC(=O)O)C(=O)O)NCc2cnc3c…
JZM RCSB PDB P0ABQ4 302.8 Da LogP 3.60 TPSA 77.8 ✓ Ro5 ✓ Clean c1cc2c(c(c1)Sc3ccc(cc3)Cl)c(nc(n2)N)N
LG3 RCSB PDB P0ABQ4 110.1 Da LogP -0.36 TPSA 77.8 ✓ Ro5 ✓ Clean c1cnc(nc1N)N
MTX RCSB PDB P0ABQ4 454.4 Da LogP 0.27 TPSA 210.5 ✓ Ro5 ✓ Clean CN(Cc1cnc2c(n1)c(nc(n2)N)N)c3ccc(cc3)C(=O)N[C@@…
N22 RCSB PDB Q81R22 312.4 Da LogP 1.81 TPSA 96.3 ✓ Ro5 ✓ Clean CCc1c(c(nc(n1)N)N)C#CCc2cc(ccc2OC)OC
PQD RCSB PDB P0ABQ4 304.4 Da LogP 2.38 TPSA 108.8 ✓ Ro5 ✓ Clean c1cc(cc(c1)N)Cn2ccc3c2ccc4c3c(nc(n4)N)N
Q24 RCSB PDB P0ABQ4 160.2 Da LogP 0.79 TPSA 77.8 ✓ Ro5 ✓ Clean c1ccc2c(c1)c(nc(n2)N)N
RAR RCSB PDB Q81R22 486.6 Da LogP 3.98 TPSA 129.0 ✓ Ro5 ✓ Clean CCC[C@H]1c2ccccc2C=NN1C(=O)\C=C\c3cc(cc(c3OC)OC…
TE RCSB PDB P0ABQ4 129.6 Da LogP -0.92 TPSA 0.0 ✓ Ro5 ✓ Clean [TeH2]
THG RCSB PDB P0ABQ4 445.4 Da LogP -0.28 TPSA 211.6 1 viol. ✓ Clean c1cc(ccc1C(=O)N[C@@H](CCC(=O)O)C(=O)O)NC[C@H]2C…
TOP RCSB PDB P0ABQ4 290.3 Da LogP 1.26 TPSA 105.5 ✓ Ro5 ✓ Clean COc1cc(cc(c1OC)OC)Cc2cnc(nc2N)N
ZM4 RCSB PDB P0ABQ4 399.5 Da LogP 3.43 TPSA 120.9 ✓ Ro5 ✓ Clean CCc1c(c(nc(n1)N)N)C#CC(C)c2cc(ccc2C)c3ccc(cc3)C…

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.

Cross-references

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

Chemistry

ChEMBL CHEMBL286400 ChEMBL CHEMBL14001 ChEMBL CHEMBL31713 ChEMBL CHEMBL31887 ChEMBL CHEMBL418347 ChEMBL CHEMBL31924 ChEMBL CHEMBL274430 ChEMBL CHEMBL13673 ChEMBL CHEMBL418293 ChEMBL CHEMBL418492 ChEMBL CHEMBL60827 ChEMBL CHEMBL13820 ChEMBL CHEMBL278345 ChEMBL CHEMBL300545 ChEMBL CHEMBL14002 ChEMBL CHEMBL30938 ChEMBL CHEMBL23609 ChEMBL CHEMBL418763 ChEMBL CHEMBL31891 ChEMBL CHEMBL13877 ChEMBL CHEMBL59416 ChEMBL CHEMBL13796 ChEMBL CO4 ChEMBL CHEMBL23338 ChEMBL CHEMBL3828485 ChEMBL U06 ChEMBL CHEMBL60069 ChEMBL CHEMBL33697 ChEMBL CP6 ChEMBL CHEMBL117105 ChEMBL CHEMBL119302 ChEMBL CHEMBL331292 ChEMBL CHEMBL118649 ChEMBL CHEMBL117584 ChEMBL CHEMBL323889 ChEMBL CHEMBL30999 ChEMBL CHEMBL58550 ChEMBL CHEMBL23746 ChEMBL CHEMBL282022 ChEMBL CHEMBL3828581 ChEMBL CHEMBL13908 ChEMBL CHEMBL3827326 ChEMBL CHEMBL3827086 ChEMBL CHEMBL321942 ChEMBL CHEMBL104369 ChEMBL CHEMBL20587 ChEMBL CHEMBL14201 ChEMBL CHEMBL119640 ChEMBL CHEMBL322001 ChEMBL CHEMBL113816 ChEMBL CHEMBL116183 ChEMBL CHEMBL105006 ChEMBL CHEMBL56719 ChEMBL CHEMBL3827760 ChEMBL CHEMBL333696 ChEMBL CHEMBL119068 ChEMBL CHEMBL20224 ChEMBL CHEMBL171639 ChEMBL CHEMBL56282 ChEMBL CHEMBL105283 ChEMBL CHEMBL118262 ChEMBL CHEMBL172805 ChEMBL CHEMBL369211 ChEMBL CHEMBL31249 ChEMBL CHEMBL117390 ChEMBL CHEMBL32039 ChEMBL CHEMBL176489 ChEMBL CHEMBL18925 ChEMBL CHEMBL284821 ChEMBL CHEMBL320596 ChEMBL CHEMBL427305 ChEMBL CHEMBL60486 ChEMBL CHEMBL114354 ChEMBL CHEMBL3828291 ChEMBL CHEMBL3828724 ChEMBL 5DR ChEMBL CHEMBL25888 ChEMBL CHEMBL423434 ChEMBL PRD ChEMBL CHEMBL332543 ChEMBL CHEMBL301236 ChEMBL CHEMBL119 ChEMBL CHEMBL134561 ChEMBL CHEMBL23532 ChEMBL CHEMBL263732 ChEMBL CHEMBL170172 ChEMBL CHEMBL412659 ChEMBL CHEMBL57787 ChEMBL CHEMBL1724189 ChEMBL CHEMBL282044 ChEMBL CHEMBL367061 ChEMBL CHEMBL57318 ChEMBL COG ChEMBL CHEMBL173641 ChEMBL CHEMBL117750 ChEMBL CHEMBL59946 ChEMBL CHEMBL303075 ChEMBL CHEMBL56318 ChEMBL CHEMBL142741 ChEMBL CHEMBL318078