X-group (possible homology)

5022 Subunit XII of photosystem I reaction centre, PsaM

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Ligands and drugs

233

Member domains

166

with ligand contacts (≤ 4 Å)

71.2% of members

with DrugDomain annotations

41.2% of members

with a DrugBank compound

38.2% 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	8.2	0	q < 0.0001
Lipids and lipid-like molecules	15	1.9	8.04×	not tested
Organoheterocyclic compounds	9	2.6	3.49×	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	75
DB02133	CLA	Chlorophyll A	41
DB02043	LHG	1,2-Dipalmitoyl-Phosphatidyl-Glycerole	25
DB03426	DGD	Digalactosyl Diacyl Glycerol (Dgdg)	2

Most frequently bound compounds

PDB ligand	Name	Domains in contact
CLA	CHLOROPHYLL A	161
BCR	BETA-CAROTENE	123
LHG	1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE	57
LMG	1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE	30
ECH	beta,beta-caroten-4-one	17
SQD	1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL	11
UNL	Unknown ligand	8
8CT	(6'R,11cis,11'cis,13cis,15cis)-4',5'-didehydro-5',6'-dihydro-beta,beta-carotene	6
A1L1F	[(2~{Z},4~{E},6~{E},8~{E},10~{E},12~{E},14~{E})-17-[(4~{S},6~{R})-4-acetyloxy-2,2,6-trimethyl-6-oxidanyl-cyclohexylidene]-6,11,15-trimethyl-2-[(~{E})-2-[(1~{S},4~{S},6~{R})-2,2,6-trimethyl-4-oxidanyl-7-oxabicyclo[4.1.0]heptan-1-yl]ethenyl]heptadeca-2,4,6,8,10,12,14,16-octaenyl] octanoate	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	6
CL7	CHLOROPHYLL D	4
45D	beta,beta-carotene-4,4'-dione	2
A86	(3S,3'S,5R,5'R,6S,6'R,8'R)-3,5'-dihydroxy-8-oxo-6',7'-didehydro-5,5',6,6',7,8-hexahydro-5,6-epoxy-beta,beta-caroten-3'-yl acetate	2
AJP	Digitonin	2
XAT	(3S,5R,6S,3'S,5'R,6'S)-5,6,5',6'-DIEPOXY-5,6,5',6'- TETRAHYDRO-BETA,BETA-CAROTENE-3,3'-DIOL	2
CHL	CHLOROPHYLL B	1
DD6	(3S,3'R,5R,6S,7cis)-7',8'-didehydro-5,6-dihydro-5,6-epoxy-beta,beta-carotene-3,3'-diol	1
DGD	DIGALACTOSYL DIACYL GLYCEROL (DGDG)	1
LMU	DODECYL-ALPHA-D-MALTOSIDE	1
ZEX	(1R,2S)-4-{(1E,3E,5E,7E,9E,11E,13E,15E,17E)-18-[(4S)-4-hydroxy-2,6,6-trimethylcyclohex-1-en-1-yl]-3,7,12,16-tetramethyloctadeca-1,3,5,7,9,11,13,15,17-nonaen-1-yl}-2,5,5-trimethylcyclohex-3-en-1-ol	1