X-group (possible homology)

3379 Photosystem II reaction center protein ycf12

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Ligands and drugs

327

Member domains

295

with ligand contacts (≤ 4 Å)

90.2% of members

180

with DrugDomain annotations

55.0% of members

147

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
Lipids and lipid-like molecules	10	1.1	9.11×	not tested
Organoheterocyclic compounds	2	1.5	1.32×	not tested
Homogeneous metal compounds	3	4.8	0.62×	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
DB06755	BCR	Beta carotene	142
DB02043	LHG	1,2-Dipalmitoyl-Phosphatidyl-Glycerole	2
DB02133	CLA	Chlorophyll A	2
DB03193	STE	Stearic acid	1
DB04450	HTG	Heptyl 1-Thiohexopyranoside	1

Most frequently bound compounds

PDB ligand	Name	Domains in contact
CLA	CHLOROPHYLL A	284
BCR	BETA-CAROTENE	277
LMG	1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE	258
UNL	Unknown ligand	17
8CT	(6'R,11cis,11'cis,13cis,15cis)-4',5'-didehydro-5',6'-dihydro-beta,beta-carotene	12
CAmetal	CALCIUM ION	10
DGA	DIACYL GLYCEROL	9
MGmetal	MAGNESIUM ION	6
WVN	1,3,3-trimethyl-2-[(1E,3E,5E,7E,9E,11E,13E,15E,17E)-3,7,12,16-tetramethyl-18-[(1R)-2,6,6-trimethylcyclohex-2-en-1-yl]octadeca-1,3,5,7,9,11,13,15,17-nonaenyl]cyclohexene	4
STE	STEARIC ACID	3
SQD	1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL	2
HEM	PROTOPORPHYRIN IX CONTAINING FE	1
HTG	heptyl 1-thio-beta-D-glucopyranoside	1
LHG	1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE	1
PLM	PALMITIC ACID	1