X-group (possible homology)

3493 Photosystem II PsbX protein

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Ligands and drugs

427

Member domains

331

with ligand contacts (≤ 4 Å)

77.5% of members

234

with DrugDomain annotations

54.8% of members

234

with a DrugBank compound

54.8% 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)

—

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
Homogeneous metal compounds	0	7.7	0	q = 1.2e-4
Hydrocarbons	1	0.1	9.07×	not tested
Lipids and lipid-like molecules	15	1.8	8.54×	not tested
Organoheterocyclic compounds	16	2.4	6.59×	not tested
Organic oxygen compounds	2	3.1	0.64×	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
DB02133	CLA	Chlorophyll A	226
DB06755	BCR	Beta carotene	191
DB03193	STE	Stearic acid	49
DB15914	RRX	Cryptoxanthin	33
DB02043	LHG	1,2-Dipalmitoyl-Phosphatidyl-Glycerole	10
DB04450	HTG	Heptyl 1-Thiohexopyranoside	7
DB03426	DGD	Digalactosyl Diacyl Glycerol (Dgdg)	2

Most frequently bound compounds

PDB ligand	Name	Domains in contact
CLA	CHLOROPHYLL A	324
BCR	BETA-CAROTENE	241
SQD	1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL	216
PL9	2,3-DIMETHYL-5-(3,7,11,15,19,23,27,31,35-NONAMETHYL-2,6,10,14,18,22,26,30,34-HEXATRIACONTANONAENYL-2,5-CYCLOHEXADIENE-1,4-DIONE-2,3-DIMETHYL-5-SOLANESYL-1,4-BENZOQUINONE	155
UNL	Unknown ligand	108
RRX	(3R)-beta,beta-caroten-3-ol	56
STE	STEARIC ACID	52
LMG	1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE	44
LHG	1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE	14
DGA	DIACYL GLYCEROL	12
8CT	(6'R,11cis,11'cis,13cis,15cis)-4',5'-didehydro-5',6'-dihydro-beta,beta-carotene	11
LFA	EICOSANE	7
CL7	CHLOROPHYLL D	6
PLM	PALMITIC ACID	4
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
3PH	1,2-DIACYL-GLYCEROL-3-SN-PHOSPHATE	2
HTG	heptyl 1-thio-beta-D-glucopyranoside	2
LNL	ALPHA-LINOLENIC ACID	2
P6G	HEXAETHYLENE GLYCOL	2
VTQ	RRR-ALPHA-TOCOPHERYLQUINONE	2