X-group (possible homology)

70 beta-clip

Open in classification tree →

Ligands and drugs

4,958

Member domains

1,111

with ligand contacts (≤ 4 Å)

22.4% of members

1,015

with DrugDomain annotations

20.5% of members

884

with a DrugBank compound

17.8% 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)

7.9

Superclasses per 20 proteins

broader 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
Nucleosides, nucleotides, and analogues	78	24.0	3.25×	q < 0.0001
Homogeneous metal compounds	63	42.6	1.48×	q < 0.0001
Organoheterocyclic compounds	15	13.4	1.12×	q = 0.73
Benzenoids	7	6.3	1.10×	q = 0.75
Homogeneous non-metal compounds	18	18.7	0.96×	q = 1.00
Organic acids and derivatives	6	13.4	0.45×	q = 0.04
Organic oxygen compounds	4	17.3	0.23×	q = 2.3e-4
Lipids and lipid-like molecules	2	9.7	0.21×	q = 0.01
Miscellaneous inorganic compounds	1	0.1	15×	not tested
Organosulfur compounds	3	1.8	1.68×	not tested
Mixed metal/non-metal compounds	2	1.8	1.10×	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
DB01752	SAH	S-adenosyl-L-homocysteine	195
DB00118	SAM	Ademetionine	172
DB01965	DUP	2'-Deoxyuridine 5'-alpha,beta-imido-triphosphate	85
DB02256	DUR	2'-Deoxyuridine	65
DB03800	UMP	Deoxyuridine monophosphate	57
DB02333	DUT	Deoxyuridine-5'-Triphosphate	40
DB03413	DUD	Deoxyuridine-5'-Diphosphate	29
DB01910	SFG	Sinefungin	28
DB02452	TTP	Thymidine 5'-triphosphate	21
DB03258	DCP	2'-Deoxycytidine 5'-triphosphate	7
DB03345	BME	Mercaptoethanol	7
DB00123	LYS	Lysine	6
DB15878	MOO	Molybdate	6
DB01714	MLZ	Epsilon-N-methyllysine	4
DB03435	UDP	Uridine-5'-Diphosphate	4
DB04685	DUX	1-{(2S,5S)-4-FLUORO-5-[(TRITYLOXY)METHYL]TETRAHYDROFURAN-2-YL}PYRIMIDINE-2,4(1H,3H)-DIONE	4
DB00131	AMP	Adenosine phosphate	3
DB03458	SA8	N(4)-Adenosyl-N(4)-methyl-2,4-diaminobutanoic acid	3
DB03977	M3L	Trimethyllysine	3
DB00130	GLN	L-Glutamine	2

Most frequently bound compounds

PDB ligand	Name	Domains in contact
ZNmetal	ZINC ION	342
SAH	S-ADENOSYL-L-HOMOCYSTEINE	224
SAM	S-ADENOSYLMETHIONINE	198
MGmetal	MAGNESIUM ION	182
DUP	2'-DEOXYURIDINE 5'-ALPHA,BETA-IMIDO-TRIPHOSPHATE	89
DUR	2'-DEOXYURIDINE	65
POP	PYROPHOSPHATE 2-	64
UMP	2'-DEOXYURIDINE 5'-MONOPHOSPHATE	63
CL	CHLORIDE ION	59
UNX	UNKNOWN ATOM OR ION	48
DUT	DEOXYURIDINE-5'-TRIPHOSPHATE	42
SFG	SINEFUNGIN	38
NAmetal	SODIUM ION	35
DUD	DEOXYURIDINE-5'-DIPHOSPHATE	29
TTP	THYMIDINE-5'-TRIPHOSPHATE	21
CAmetal	CALCIUM ION	13
NImetal	NICKEL (II) ION	12
SCN	THIOCYANATE ION	10
BME	BETA-MERCAPTOETHANOL	8
LYS	LYSINE	8