X-group (possible homology)

2494 DTD-like

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Ligands and drugs

884

Member domains

199

with ligand contacts (≤ 4 Å)

22.5% of members

199

with DrugDomain annotations

22.5% of members

123

with a DrugBank compound

13.9% 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
Organic acids and derivatives	6	1.5	3.93×	not tested
Nucleosides, nucleotides, and analogues	4	2.7	1.47×	not tested
Homogeneous non-metal compounds	3	2.1	1.41×	not tested
Benzenoids	1	0.7	1.39×	not tested
Homogeneous metal compounds	6	4.8	1.24×	not tested
Organic oxygen compounds	1	2.0	0.51×	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
DB04024	A3S	Serine-3'-aminoadenosine	20
DB16833	ADP	Adenosine disphosphate	13
DB03929	DSN	D-Serine	4
DB04742	NCF	(2R)-2-{(1R)-2-oxo-1-[(2-thienylacetyl)amino]ethyl}-5,6-dihydro-2h-1,3-thiazine-4-carboxylic acid	4
DB02517	DGL	D-Glutamic Acid	2
DB03252	DLY	D-Lysine	2
DB03355	TSB	5'-O-(L-Threonylsulfamoyl)adenosine	2
DB03869	SSA	5'-O-(L-Serylsulfamoyl)adenosine	2
DB04027	DAR	D-arginine	2
DB00133	SER	Serine	1

Most frequently bound compounds

PDB ligand	Name	Domains in contact
MGmetal	MAGNESIUM ION	30
A3S	SERINE-3'-AMINOADENOSINE	20
A3T	3'-deoxy-3'-(L-threonylamino)adenosine	15
COmetal	COBALT (II) ION	14
IOD	IODIDE ION	14
ADP	ADENOSINE-5'-DIPHOSPHATE	13
A3G	3'-deoxy-3'-(glycylamino)adenosine	10
D3Y	3'-deoxy-3'-(D-tyrosylamino)adenosine	10
REZ	(2R)-2-AMINO-7-{[(1R)-1-CARBOXYETHYL]AMINO}-7-OXOHEPTANOIC ACID	5
B07	2,6 DIMETHOXYBENZAMIDOBORONIC ACID	4
BH6	{[(2-chlorobenzoyl)amino]methyl}boronic acid	4
BIY	(3S)-2,2-dimethyl-3,4-dihydro-2H-1,4-thiazine-3,6-dicarboxylic acid	4
EWA	[(1S)-1-{[(2,6-DIMETHOXYPHENYL)CARBONYL]AMINO}ETHYL]BORONIC ACID	4
EWB	[(1S)-1-{[(2-benzylphenyl)carbonyl]amino}ethyl](trihydroxy)borate(1-)	4
HQZ	trihydroxy{(1S)-1-[(methylsulfonyl)amino]ethyl}borate(1-)	4
NCF	(2R)-2-{(1R)-2-OXO-1-[(2-THIENYLACETYL)AMINO]ETHYL}-5,6-DIHYDRO-2H-1,3-THIAZINE-4-CARBOXYLIC ACID	4
REC	CEPHALOSPORIN	4
TFR	(2R)-2-amino-7-oxo-7-{[(2R,3S)-4,4,4-trifluoro-3-hydroxybutan-2-yl]amino}heptanoic acid	4
ZA3	TRIHYDROXY-[[(2-NITROPHENYL)CARBONYLAMINO]METHYL]BORON	4
ZNmetal	ZINC ION	4