X-group (possible homology)

279 LDH C-terminal domain-like

Open in classification tree →

Ligands and drugs

2,285

Member domains

981

with ligand contacts (≤ 4 Å)

42.9% of members

897

with DrugDomain annotations

39.3% of members

735

with a DrugBank compound

32.2% 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)

7.4

Superclasses per 20 proteins

narrower than 53% of the 256 X-groups with enough proteins to compare (median 7.6)

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
Organic acids and derivatives	37	11.9	3.11×	q < 0.0001
Nucleosides, nucleotides, and analogues	61	21.3	2.87×	q < 0.0001
Organic oxygen compounds	15	15.3	0.98×	q = 1.00
Organoheterocyclic compounds	8	11.8	0.68×	q = 0.34
Homogeneous non-metal compounds	11	16.6	0.67×	q = 0.23
Homogeneous metal compounds	22	37.8	0.58×	q = 1.0e-3
Benzenoids	3	5.6	0.53×	q = 0.46
Lipids and lipid-like molecules	0	8.6	0	q = 5.5e-4
Lignans, neolignans and related compounds	1	0.1	17×	not tested
Organosulfur compounds	2	1.6	1.26×	not tested
Phenylpropanoids and polyketides	1	1.6	0.63×	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	269
DB00157	NAI	NADH	175
DB03940	OXM	Oxamic Acid	88
DB04551	FBP	beta-D-fructofuranose 1,6-bisphosphate	35
DB00119	PYR	Pyruvic acid	25
DB02637	OAA	Oxaloacetate Ion	15
DB03066	LAC	D-Lactic acid	13
DB02007	G6P	alpha-D-glucose 6-phosphate	11
DB02401	OXQ	4-Hydroxy-1,2,5-oxadiazole-3-carboxylic acid	11
DB02175	MLA	Malonic acid	10
DB03363	A3D	3-Acetylpyridine Adenine Dinucleotide	10
DB14475	2OP	L-Lactic acid	8
DB16833	ADP	Adenosine disphosphate	7
DB01677	FUM	Fumaric acid	6
DB02338	NDP	NADPH	6
DB03461	NAP	Nicotinamide adenine dinucleotide phosphate	5
DB00117	HIS	Histidine	3
DB02249	ETX	2-Ethoxyethanol	3
DB03709	BCN	Bicine	3
DB11091	PEO	Hydrogen peroxide	3

Most frequently bound compounds

PDB ligand	Name	Domains in contact
NAD	NICOTINAMIDE-ADENINE-DINUCLEOTIDE	283
NAI	1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE	191
OXM	OXAMIC ACID	112
CL	CHLORIDE ION	68
FBP	1,6-di-O-phosphono-beta-D-fructofuranose	44
NDP	NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE	36
MNmetal	MANGANESE (II) ION	25
PYR	PYRUVIC ACID	25
NAmetal	SODIUM ION	22
AGmetal	SILVER ION	20
G6P	6-O-phosphono-alpha-D-glucopyranose	18
CAmetal	CALCIUM ION	15
OAA	OXALOACETATE ION	15
LAC	LACTIC ACID	13
6V0	[[(2~{R},3~{S},4~{R},5~{R})-5-(5-aminocarbonyl-2~{H}-pyridin-1-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] [(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methyl hydrogen phosphate	12
LMR	(2S)-2-hydroxybutanedioic acid	12
CDmetal	CADMIUM ION	11
MLA	MALONIC ACID	11
OXQ	4-HYDROXY-1,2,5-OXADIAZOLE-3-CARBOXYLIC ACID	11
A3D	3-ACETYLPYRIDINE ADENINE DINUCLEOTIDE	10