Protein target profile

KP13_04549

NAD-dependent malic enzyme

Genome: KpKP13 Gene: sfcA AHE44424.1 3D evidence: AlphaFold DB model + ColabFold model UniProt A0A0H3GTA5
Length 565
Pocket druggability 0.636
Direct ligand evidence 0 65 total records
Functional annotation 1 EC 7 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 (%)
48.56 Lower values reduce human off-target concern.
Human E-value
9.06e-81
Gut microbiome similarity
2.7% of screened genomes Lower prevalence suggests narrower overlap with the screened gut microbiome.

Essentiality

Essential (DEG)
Y
DEG identity (%)
42.435 Higher values support similarity to known essential genes.
DEG E-value
8.77e-158 Smaller values mean stronger essential-gene similarity.

Localization

Localization
CytoplasmicMembrane

Structure confidence

ColabFold pLDDT
95.19 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 0.636
Structure A0A0H3GTA5
Pocket Pocket 31
P2Rank 0.898
Structure A0A0H3GTA5
Pocket Pocket 1
ColabFold model
FPocket 0.899 · Pocket 25
P2Rank 0.896 · Pocket 1
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 128 / 4744 genomes with a hit
Prevalence 2.7%

Cross-references

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

Sequence

Primary amino-acid sequence viewer.

MQFTHKKNRSLYIPYAGPVLLEFPLLNKGSAFSMEERSNFNLLGLLPEVVETIEEQAERAWIQYQGFKTEIDKHIYLRNIQDTNETLFYRLIGNHLEEMMPVIYTPTVGAACERFSEIYRRARGVFISYQNRHNLDDILQNVPNHNVKVIVVTDGERILGLGDQGIGGMGIPIGKLSLYTTCGGISPAYTLPIVLDVGTNNQQLLDDPLYMGWRHPRITDDEYYQFVDDVIQAIKARWPDVLLQFEDFAQKNAMPLLNRYRNEICSFNDDIQGTAAVTVGTLIAASRGAGSQLSEQKIVFLGAGSAGCGIAEQIIAQIVREGLSEEEARQRVFMVDRFGLLTDGMPNLLPFQNKLVQKREQLQSWDTTSEALSLLDVVRNVKPNILIGVSGQPGLFTEEIIREMHKHCPRPIVMPLSNPTSRVEATPQNILSWTDGEALVATGSPFSPVTVKGKQYPIAQCNNSYIFPGIGLGVIASGASRVTDEMLMAASETLAQHSPLVNNGEGPVLPELKDIQTVSRAIAFAVGKVAQEQGVAVKTSAEALLQAISDNFWLPEYRNYRRTSI

Functional annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 7 GO

Enzyme Commission (EC)

1

Gene Ontology (GO)

7
  • 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:0004470 Catalysis of the oxidative decarboxylation of malate with the concomitant production of pyruvate.
  • GO:0004471 Catalysis of the reaction: (S)-malate + NAD+ = pyruvate + CO2 + NADH.
  • GO:0005829 The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
  • GO:0046872 Binding to a metal ion.
  • GO:0008948 Catalysis of the reaction: H+ + oxaloacetate = CO2 + pyruvate.
  • GO:0006108 The chemical reactions and pathways involving malate, the anion of hydroxybutanedioic acid, a chiral hydroxydicarboxylic acid. The (+) enantiomer is an important intermediate in metabolism as a component of both the TCA cycle and the glyoxylate cycle.

Sequence domains and features

Domain and signature matches imported from InterPro and related databases.

38 records
Show feature table
Start End DB Term Name
81 261 SMART SM01274 malic_2
81 261 InterPro IPR012301 Malic enzyme, N-terminal domain
16 268 FunFam G3DSA:3.40.50.10380:FF:000001 NAD-dependent malic enzyme
81 261 Pfam PF00390 Malic enzyme, N-terminal domain
271 562 SUPERFAMILY SSF51735 NAD(P)-binding Rossmann-fold domains
271 562 InterPro IPR036291 NAD(P)-binding domain superfamily
5 270 SUPERFAMILY SSF53223 Aminoacid dehydrogenase-like, N-terminal domain
5 270 InterPro IPR046346 Aminoacid dehydrogenase-like, N-terminal domain superfamily
4 565 Hamap MF_01619 NAD-dependent malic enzyme [maeA].
4 565 InterPro IPR023667 NAD-dependent malic enzyme, proteobacteria
2 563 PIRSF PIRSF000106 ME
2 563 InterPro IPR001891 Malic oxidoreductase
271 531 SMART SM00919 Malic_M_2
271 531 InterPro IPR012302 Malic enzyme, NAD-binding
271 555 CDD cd05312 NAD_bind_1_malic_enz
14 560 PANTHER PTHR23406 MALIC ENZYME-RELATED
271 530 Pfam PF03949 Malic enzyme, NAD binding domain
271 530 InterPro IPR012302 Malic enzyme, NAD-binding
269 564 FunFam G3DSA:3.40.50.720:FF:000055 NAD-dependent malic enzyme
16 268 Gene3D G3DSA:3.40.50.10380 -
16 268 InterPro IPR037062 Malic enzyme, N-terminal domain superfamily
269 564 Gene3D G3DSA:3.40.50.720 -
267 283 PRINTS PR00072 Malic enzyme signature
267 283 InterPro IPR001891 Malic oxidoreductase
87 111 PRINTS PR00072 Malic enzyme signature
87 111 InterPro IPR001891 Malic oxidoreductase
183 205 PRINTS PR00072 Malic enzyme signature
183 205 InterPro IPR001891 Malic oxidoreductase
408 424 PRINTS PR00072 Malic enzyme signature
408 424 InterPro IPR001891 Malic oxidoreductase
147 176 PRINTS PR00072 Malic enzyme signature
147 176 InterPro IPR001891 Malic oxidoreductase
298 314 PRINTS PR00072 Malic enzyme signature
298 314 InterPro IPR001891 Malic oxidoreductase
242 260 PRINTS PR00072 Malic enzyme signature
242 260 InterPro IPR001891 Malic oxidoreductase
267 283 ProSitePatterns PS00331 Malic enzymes signature.
267 283 InterPro IPR015884 Malic enzyme, conserved site

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 · FPocket

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

Site 1 FPocket #31
0.636
Likely same site as P2Rank 1 2.9 Å 25 shared residues 89% of smaller site
Unusual size
Show in viewer
Surrounding area
Site 2 FPocket #1
0.565
Likely same site as P2Rank 4 0.9 Å 14 shared residues 100% of smaller site
Show in viewer
Surrounding area

Binding pockets · P2Rank

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

Site 1 P2Rank #1
0.898
Likely same site as FPocket 31 2.9 Å 25 shared residues 89% of smaller site
Show in viewer
Surrounding area
Site 2 P2Rank #2
0.372
Show in viewer
Surrounding area
Site 3 P2Rank #3
0.334
Show in viewer
Surrounding area
Site 4 P2Rank #4
0.276
Likely same site as FPocket 1 0.9 Å 14 shared residues 100% of smaller site
Show in viewer
Surrounding area
Site 5 P2Rank #5
0.188
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Surrounding area
Residue sets
UniProt: Active site:104-104 Proton donor
UniProt: Active site:175-175 Proton acceptor
UniProt: Binding site:157-157
UniProt: Binding site:246-246
UniProt: Binding site:247-247
UniProt: Binding site:270-270
UniProt: Binding site:418-418
UniProt: Binding site:462-462
UniProt: Site:270-270 Important for activity
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_A0A0H3GTA5
AlphaFold DB full sequence Viewing
ColabFold KP13_04549
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.

65 records
Chemistry signal

Structural and bioactivity evidence are both available for this target.

Direct evidence 0 same-protein records
Transferred evidence 15 records from similar proteins
Structural ligands 13 0 loaded crystals
Measured bioactivity 2 direct and transferred ChEMBL records
Proposed compounds 50 similarity-based ZINC candidates
Best available ligand signal
FUM PDB via homolog 116.1 Da · LogP -0.29 · TPSA 74.6 Open detail RCSB PDB
MAK PDB via homolog Detail RCSB PDB
MLT PDB via homolog Detail RCSB PDB
OXL PDB via homolog Detail RCSB PDB
PYR 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
FUM RCSB PDB P23368 116.1 Da LogP -0.29 TPSA 74.6 ✓ Ro5 ✓ Clean C(=C/C(=O)O)\C(=O)O
MAK RCSB PDB P23368 118.0 Da LogP -1.28 TPSA 91.7 ✓ Ro5 ✓ Clean C(=O)(C(=O)O)C(=O)O
MLT RCSB PDB P23368 134.1 Da LogP -1.09 TPSA 94.8 ✓ Ro5 ✓ Clean C([C@H](C(=O)O)O)C(=O)O
OXL RCSB PDB P23368 88.0 Da LogP -3.51 TPSA 80.3 ✓ Ro5 ✓ Clean C(=O)(C(=O)[O-])[O-]
PYR RCSB PDB P23368 88.1 Da LogP -0.34 TPSA 54.4 ✓ Ro5 ✓ Clean CC(=O)C(=O)O
SEV RCSB PDB Q4DJ68 418.4 Da LogP 4.03 TPSA 84.5 ✓ Ro5 ✓ Clean COc1ccc(cc1)NS(=O)(=O)c2cccc(c2)NC(=O)c3cc(cc(c…
SJD RCSB PDB Q4DJ68 436.4 Da LogP 4.17 TPSA 84.5 ✓ Ro5 ✓ Clean COc1ccc(c(c1)F)NS(=O)(=O)c2cccc(c2)NC(=O)c3cc(c…
SWV RCSB PDB Q4DJ68 372.4 Da LogP 2.67 TPSA 101.1 ✓ Ro5 ✓ Clean c1ccc(c(c1)NS(=O)(=O)c2cccc(c2)NC(=O)c3cnccn3)F
SZD RCSB PDB Q4DJ68 472.4 Da LogP 4.92 TPSA 84.5 ✓ Ro5 ✓ Clean c1cc(cc(c1)S(=O)(=O)Nc2ccc(cc2)OC(F)(F)F)NC(=O)…
SZG RCSB PDB Q4DJ68 488.8 Da LogP 5.27 TPSA 84.5 1 viol. ✓ Clean c1cc(ccc1NS(=O)(=O)c2ccc(c(c2)NC(=O)c3cc(cc(c3)…
SZJ RCSB PDB Q4DJ68 454.4 Da LogP 4.62 TPSA 84.5 ✓ Ro5 ✓ Clean c1cc(cc(c1)S(=O)(=O)Nc2ccc(cc2)OC(F)F)NC(=O)c3c…
SZP RCSB PDB Q4DJ68 506.8 Da LogP 5.57 TPSA 84.5 2 viol. ✓ Clean c1cc(ccc1NS(=O)(=O)c2ccc(c(c2)NC(=O)c3cc(cc(c3)…
TTN RCSB PDB P27443 118.0 Da LogP -4.15 TPSA 100.5 ✓ Ro5 ✓ Clean C(C(=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.