X-group (possible homology)

7073 C-terminal domain of Malic enzyme

Open in classification tree →

Ligands and drugs

218

Member domains

108

with ligand contacts (≤ 4 Å)

49.5% of members

103

with DrugDomain annotations

47.2% of members

with a DrugBank compound

45.0% of members

Aggregated over all current member domains of this group. Drug annotations come from DrugDomain; buffers and crystallization additives are excluded from the tables below.

Chemical profile

ClassyFire chemical superclasses of the ligands bound by this X-group's proteins, from DrugDomain annotations.

Proteins with classified ligands

Superclasses bound (of 23)

—

Superclasses per 20 proteins

fewer than 20 proteins: too few to compare at equal depth

The raw number of superclasses rises with the number of proteins sampled; the per-20 value compares X-groups at equal depth.

Superclass	Proteins	Expected	Ratio	Significance
Nucleosides, nucleotides, and analogues	5	1.4	3.67×	not tested
Organoheterocyclic compounds	1	0.8	1.32×	not tested
Organic acids and derivatives	1	0.8	1.31×	not tested
Organic oxygen compounds	1	1.0	1.02×	not tested
Homogeneous non-metal compounds	1	1.1	0.94×	not tested
Homogeneous metal compounds	2	2.4	0.83×	not tested

enriched (q < 0.05)depleted (q < 0.05)not significantnot tested (expected < 5)

Unit: a protein (UniProt accession) with a ligand-binding domain in this X-group, counted once per superclass. Expected counts use each superclass's frequency across all ligand-binding X-groups; significance is Fisher's exact test with Benjamini–Hochberg correction. Buffers and crystallization additives are excluded. ECOD v295.2; the method follows the ECOD 2027 update, whose published figures used a slightly different artifact filter.

DrugBank compounds

DrugBank	PDB ligand	Name	Domains
DB14128	NAD	Nadide	46
DB03461	NAP	Nicotinamide adenine dinucleotide phosphate	22
DB03680	TTN	Tartronate	10
DB00171	ATP	ATP	8
DB02338	NDP	NADPH	8
DB00157	NAI	NADH	6
DB00119	PYR	Pyruvic acid	4
DB03589	MAK	Mesoxalic acid	4

Most frequently bound compounds

PDB ligand	Name	Domains in contact
NAD	NICOTINAMIDE-ADENINE-DINUCLEOTIDE	48
NAP	NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE	25
NAmetal	SODIUM ION	10
TTN	TARTRONATE	10
CL	CHLORIDE ION	9
ATP	ADENOSINE-5'-TRIPHOSPHATE	8
NDP	NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE	8
86I	6-[(7-methyl-2-propyl-imidazo[4,5-b]pyridin-4-yl)methyl]-2-[2-(1H-1,2,3,4-tetrazol-5-yl)phenyl]-1,3-benzothiazole	4
LMR	(2S)-2-hydroxybutanedioic acid	4
MAK	ALPHA-KETOMALONIC ACID	4
NAI	1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE	4
PYR	PYRUVIC ACID	4
A1AE5	2~3~,2~6~-dihydroxy-1~4~,3~4~-dimethoxy[1~1~,2~1~:2~4~,3~1~-terphenyl]-2~2~,2~5~-dione	2
SIN	SUCCINIC ACID	2
MNmetal	MANGANESE (II) ION	1