Protein profile

KP13_03840

NADP-dependent malic enzyme

Genome: KpKP13

Gene: maeB AHE43324.1 Structure source: AlphaFold + ColabFold UniProt A0A0H3GRH5
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Amino acids 759
Annotations 8
Features 32
PDB binders 10
Druggability 0.811

Overview

Basic information about this protein and its source genome.

Accession
KP13_03840
Assembly
Klebsiella pneumoniae subsp. pneumoniae Kp13, complete sequence
Gene
maeB AHE43324.1
Status
annotated
Amino acids
759
Structure source
AlphaFold + ColabFold
EC
1.1.1.40
GO
GO:0016746 Catalysis of the transfer of an acyl group from one compound (donor) to another (acceptor). 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. GO:0046872 Binding to a metal ion. GO:0004471 Catalysis of the reaction: (S)-malate + NAD+ = pyruvate + CO2 + NADH. 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.

Target profile

Computed evidence for target prioritization.

Human off-target
hit
Human identity (%)
26.087
Human E-value
2.8e-13
Gut microbiome off-target
hit
Essential (DEG)
Y
DEG identity (%)
69.485
DEG E-value
0.0
Localization
Cytoplasmic
ColabFold pLDDT
91.54

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 0.811
Structure A0A0H3GRH5
Pocket Pocket 37
P2Rank 0.906
Structure A0A0H3GRH5
Pocket Pocket 1
ColabFold model
FPocket 0.747 · Pocket 24
P2Rank 0.86 · Pocket 1
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 165 / 4744 genomes with a hit
Normalized 0.035

Sequence

Primary amino-acid sequence viewer.

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:0016746 Catalysis of the transfer of an acyl group from one compound (donor) to another (acceptor).
  • 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.
  • GO:0046872 Binding to a metal ion.
  • GO:0004471 Catalysis of the reaction: (S)-malate + NAD+ = pyruvate + CO2 + NADH.
  • 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:0004473 Catalysis of the reaction: (S)-malate + NADP+ = pyruvate + CO2 + NADPH.

Sequence Features

Domain/signature hits from InterPro and related databases.

32 records
Show feature table
Start End DB Term Name
10 161 SUPERFAMILY SSF53223 Aminoacid dehydrogenase-like, N-terminal domain
10 161 InterPro IPR046346 Aminoacid dehydrogenase-like, N-terminal domain superfamily
159 175 ProSitePatterns PS00331 Malic enzymes signature.
159 175 InterPro IPR015884 Malic enzyme, conserved site
165 360 Pfam PF03949 Malic enzyme, NAD binding domain
165 360 InterPro IPR012302 Malic enzyme, NAD-binding
573 728 Gene3D G3DSA:3.40.50.10750 -
573 728 InterPro IPR042112 Phosphate acetyltransferase, domain 2
430 754 SUPERFAMILY SSF53659 Isocitrate/Isopropylmalate dehydrogenase-like
1 758 PIRSF PIRSF036684 ME_PTA
1 758 InterPro IPR012188 NAD(P)-dependent malic enzyme
446 752 Gene3D G3DSA:3.40.50.10950 -
446 752 InterPro IPR042113 Phosphate acetyltransferase, domain 1
19 151 Pfam PF00390 Malic enzyme, N-terminal domain
19 151 InterPro IPR012301 Malic enzyme, N-terminal domain
163 400 CDD cd05311 NAD_bind_2_malic_enz
163 400 InterPro IPR045213 Malic enzyme, NAD-binding domain, bacterial type
161 445 Gene3D G3DSA:3.40.50.720 -
1 160 FunFam G3DSA:3.40.50.10380:FF:000003 NADP-dependent malic enzyme
573 728 FunFam G3DSA:3.40.50.10750:FF:000002 NADP-dependent malic enzyme
1 160 Gene3D G3DSA:3.40.50.10380 -
1 160 InterPro IPR037062 Malic enzyme, N-terminal domain superfamily
430 751 Pfam PF01515 Phosphate acetyl/butaryl transferase
430 751 InterPro IPR002505 Phosphate acetyl/butaryl transferase
163 453 SUPERFAMILY SSF51735 NAD(P)-binding Rossmann-fold domains
163 453 InterPro IPR036291 NAD(P)-binding domain superfamily
163 401 SMART SM00919 Malic_M_2
163 401 InterPro IPR012302 Malic enzyme, NAD-binding
2 432 PANTHER PTHR43237 NADP-DEPENDENT MALIC ENZYME
18 151 SMART SM01274 malic_2
18 151 InterPro IPR012301 Malic enzyme, N-terminal domain
161 444 FunFam G3DSA:3.40.50.720:FF:000095 NADP-dependent malic enzyme

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_A0A0H3GRH5
AlphaFold — — full sequence — Viewing
ColabFold KP13_03840
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
37 0.811
1 0.213

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 15.64 0.758
2 4.49 0.192
3 3.5 0.128
4 2.25 0.056
5 2.23 0.054

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.

62 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
PYR
6C7N
Q84LQ5 88.1 Da LogP -0.34 TPSA 54.4 ✓ Ro5 ✓ Clean CC(=O)C(=O)O
SEV
6W29
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
6W2N
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
6W49
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
6W59
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
6W57
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
6W56
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
6W53
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
1O0S
P27443 118.0 Da LogP -4.15 TPSA 100.5 ✓ Ro5 ✓ Clean C(C(=O)[O-])(C(=O)[O-])O
UVW
1XCO
P39646 140.0 Da LogP -0.36 TPSA 83.8 ✓ Ro5 ✓ Clean CC(=O)OP(=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.