X-group (possible homology)

5037 Bacterial photosystem II reaction centre L and M subunits-like

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Ligands and drugs

2,292

Member domains

1,643

with ligand contacts (≤ 4 Å)

71.7% of members

1,284

with DrugDomain annotations

56.0% of members

1,272

with a DrugBank compound

55.5% 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.

134

Proteins with classified ligands

Superclasses bound (of 23)

5.9

Superclasses per 20 proteins

narrower than 75% 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
Lipids and lipid-like molecules	134	14.7	9.11×	q < 0.0001
Organoheterocyclic compounds	127	20.3	6.25×	q < 0.0001
Homogeneous metal compounds	80	64.9	1.23×	q = 0.02
Homogeneous non-metal compounds	32	28.4	1.13×	q = 0.54
Organic oxygen compounds	10	26.3	0.38×	q = 3.7e-4
Organic acids and derivatives	2	20.4	0.10×	q < 0.0001
Benzenoids	0	9.7	0	q = 2.3e-4
Nucleosides, nucleotides, and analogues	0	36.5	0	q < 0.0001
Hydrocarbons	7	0.9	7.58×	not tested
Organic nitrogen compounds	1	4.2	0.24×	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	792
DB02133	CLA	Chlorophyll A	785
DB02043	LHG	1,2-Dipalmitoyl-Phosphatidyl-Glycerole	693
DB03426	DGD	Digalactosyl Diacyl Glycerol (Dgdg)	509
DB01853	BCL	Bacteriochlorophyll A	351
DB01022	PQN	Phylloquinone	344
DB09270	U10	Ubidecarenone	297
DB03429	CDL	Tetrastearoyl cardiolipin	165
DB03193	STE	Stearic acid	100
DB04450	HTG	Heptyl 1-Thiohexopyranoside	83
DB04079	HTO	Heptane-1,2,3-Triol	72
DB13075	MQ7	Menaquinone 7	56
DB08690	UQ2	Ubiquinone Q2	29
DB01728	PEF	1,2-dihexadecanoyl-sn-glycero-3-phosphoethanolamine	19
DB04735	MGE	Monogalactosyldiacylglycerol	18
DB08689	UQ1	Ubiquinone Q1	17
DB03831	MPG	[(Z)-octadec-9-enyl] (2R)-2,3-bis(oxidanyl)propanoate	12
DB03279	LMU	Dodecyl-Alpha-D-Maltoside	10
DB00137	LUT	(3R,3'R,6S)-4,5-DIDEHYDRO-5,6-DIHYDRO-BETA,BETA-CAROTENE-3,3'-DIOL	8
DB15914	RRX	Cryptoxanthin	8

Most frequently bound compounds

PDB ligand	Name	Domains in contact
CLA	CHLOROPHYLL A	1,120
BCR	BETA-CAROTENE	1,049
LHG	1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE	960
LMG	1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE	847
FE2metal	FE (II) ION	756
DGD	DIGALACTOSYL DIACYL GLYCEROL (DGDG)	747
PHO	PHEOPHYTIN A	683
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	636
SQD	1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL	601
CL	CHLORIDE ION	565
SF4	IRON/SULFUR CLUSTER	462
PQN	PHYLLOQUINONE	442
BCL	BACTERIOCHLOROPHYLL A	424
FEmetal	FE (III) ION	395
BPH	BACTERIOPHEOPHYTIN A	390
U10	UBIQUINONE-10	322
OEX	CA-MN4-O5 CLUSTER	273
UNL	Unknown ligand	265
CL0	CHLOROPHYLL A ISOMER	264
CDL	CARDIOLIPIN	207