X-group (possible homology)

7510 Isocitrate/Isopropylmalate dehydrogenase-like

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Ligands and drugs

4,527

Member domains

1,160

with ligand contacts (≤ 4 Å)

25.6% of members

1,062

with DrugDomain annotations

23.5% of members

787

with a DrugBank compound

17.4% 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)

7.6

Superclasses per 20 proteins

narrower than 51% 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	31	10.8	2.86×	q < 0.0001
Nucleosides, nucleotides, and analogues	39	19.4	2.02×	q < 0.0001
Lipids and lipid-like molecules	12	7.8	1.54×	q = 0.18
Homogeneous metal compounds	50	34.4	1.46×	q = 5.7e-4
Homogeneous non-metal compounds	14	15.1	0.93×	q = 0.93
Benzenoids	3	5.1	0.59×	q = 0.57
Organic oxygen compounds	5	13.9	0.36×	q = 0.01
Organoheterocyclic compounds	3	10.8	0.28×	q = 0.01
Organosulfur compounds	2	1.4	1.39×	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
DB03461	NAP	Nicotinamide adenine dinucleotide phosphate	194
DB02338	NDP	NADPH	119
DB08845	AKG	Oxogluric acid	95
DB14128	NAD	Nadide	91
DB04279	IPM	3-Isopropylmalic Acid	61
DB00157	NAI	NADH	30
DB00131	AMP	Adenosine phosphate	19
DB01992	COA	Coenzyme A	12
DB16833	ADP	Adenosine disphosphate	12
DB02897	UVW	Acetylphosphate	9
DB17097	9UO	Vorasidenib	9
DB02175	MLA	Malonic acid	8
DB18745	7SU	Safusidenib	8
DB00171	ATP	ATP	6
DB03434	MPO	3-(N-morpholino)propanesulfonic acid	6
DB03709	BCN	Bicine	5
DB00125	ARG	Arginine	4
DB01727	—	Isocitric Acid	4
DB03170	COD	Dephospho Coenzyme A	4
DB04349	PGO	(S)-propane-1,2-diol	4

Most frequently bound compounds

PDB ligand	Name	Domains in contact
NAP	NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE	205
ICT	ISOCITRIC ACID	187
MGmetal	MAGNESIUM ION	147
CAmetal	CALCIUM ION	118
NDP	NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE	111
AKG	2-OXOGLUTARIC ACID	103
NAD	NICOTINAMIDE-ADENINE-DINUCLEOTIDE	90
IPM	3-ISOPROPYLMALIC ACID	64
MNmetal	MANGANESE (II) ION	49
CL	CHLORIDE ION	48
ZNmetal	ZINC ION	42
ACO	ACETYL COENZYME *A	29
NAI	1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE	28
AMP	ADENOSINE MONOPHOSPHATE	16
EE1	(3~{S})-3-[(4~{S})-3-aminocarbonyl-1-[(2~{R},3~{R},4~{S},5~{R})-5-[[[[(2~{R},3~{R},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3-oxidanyl-4-phosphonooxy-oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-oxidanyl-phosphoryl]oxymethyl]-3,4-bis(oxidanyl)oxolan-2-yl]-4~{H}-pyridin-4-yl]-2-oxidanylidene-pentanedioic acid	14
NAmetal	SODIUM ION	14
COA	COENZYME A	12
DHB	3,4-DIHYDROXYBENZOIC ACID	12
SCN	THIOCYANATE ION	12
ZT3	N-(4-tert-butylphenyl)-7,8-dimethyl-5,11-dihydro-6H-pyrido[2,3-b][1,5]benzodiazepine-6-carboxamide	12