X-group (possible homology)
5077 Chlorophyll a-b binding protein
Ligands and drugs
1,789
Member domains
1,547
with ligand contacts (≤ 4 Å)
86.5% of members
709
with DrugDomain annotations
39.6% of members
709
with a DrugBank compound
39.6% 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.
153
Proteins with classified ligands
7
Superclasses bound (of 23)
4.0
Superclasses per 20 proteins
narrower than 90% 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 | 0.25×observed / expected4× | Ratio | Significance |
|---|---|---|---|---|---|
| Lipids and lipid-like molecules | 144 | 16.8 | 8.57× | q < 0.0001 | |
| Organoheterocyclic compounds | 153 | 23.2 | 6.59× | q < 0.0001 | |
| Organic oxygen compounds | 4 | 30.0 | 0.13× | q < 0.0001 | |
| Organic acids and derivatives | 3 | 23.3 | 0.13× | q < 0.0001 | |
| Benzenoids | 1 | 11.0 | 0.09× | q = 6.7e-4 | |
| Homogeneous metal compounds | 4 | 74.1 | 0.05× | q < 0.0001 | |
| Homogeneous non-metal compounds | 0 | 32.5 | 0 | q < 0.0001 | |
| Nucleosides, nucleotides, and analogues | 0 | 41.7 | 0 | q < 0.0001 | |
| Organic nitrogen compounds | 7 | 4.8 | 1.46× | 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 | 689 |
| DB04506 | CHL | Chlorophyll B | 555 |
| DB02043 | LHG | 1,2-Dipalmitoyl-Phosphatidyl-Glycerole | 544 |
| DB00137 | LUT | (3R,3'R,6S)-4,5-DIDEHYDRO-5,6-DIHYDRO-BETA,BETA-CAROTENE-3,3'-DIOL | 504 |
| DB03460 | XAT | Violaxanthin | 381 |
| DB06755 | BCR | Beta carotene | 239 |
| DB03279 | LMU | Dodecyl-Alpha-D-Maltoside | 64 |
| DB03426 | DGD | Digalactosyl Diacyl Glycerol (Dgdg) | 54 |
| DB15462 | A86 | Fucoxanthin | 51 |
| DB03796 | PLM | Palmitic Acid | 18 |
| DB15914 | RRX | Cryptoxanthin | 11 |
| DB04038 | ERG | Ergosterol | 7 |
| DB01707 | LAP | L-Alfa-Lysophosphatidylcholine, Lauroyl | 6 |
| DB03690 | PCW | (Z,Z)-4-Hydroxy-N,N,N-Trimethyl-10-Oxo-7-[(1-Oxo-9-Octadecenyl)Oxy]-3,5,9-Trioxa-4-Phosphaheptacos-18-En-1-Aminium-4-Oxide | 6 |
| DB00144 | P5S | Phosphatidyl serine | 5 |
| DB02379 | BGC | Beta-D-Glucose | 4 |
| DB02451 | BNG | B-nonylglucoside | 4 |
| DB00163 | VIV | Vitamin E | 2 |
| DB02515 | G3P | sn-glycerol 3-phosphate | 2 |
| DB04450 | HTG | Heptyl 1-Thiohexopyranoside | 2 |
Most frequently bound compounds
| PDB ligand | Name | Domains in contact |
|---|---|---|
| CLA | CHLOROPHYLL A | 1,530 |
| LHG | 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE | 995 |
| CHL | CHLOROPHYLL B | 832 |
| LUT | (3R,3'R,6S)-4,5-DIDEHYDRO-5,6-DIHYDRO-BETA,BETA-CAROTENE-3,3'-DIOL | 712 |
| 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 | 577 |
| LMG | 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE | 501 |
| NEX | (1R,3R)-6-{(3E,5E,7E,9E,11E,13E,15E,17E)-18-[(1S,4R,6R)-4-HYDROXY-2,2,6-TRIMETHYL-7-OXABICYCLO[4.1.0]HEPT-1-YL]-3,7,12,16-TETRAMETHYLOCTADECA-1,3,5,7,9,11,13,15,17-NONAENYLIDENE}-1,5,5-TRIMETHYLCYCLOHEXANE-1,3-DIOL | 422 |
| BCR | BETA-CAROTENE | 382 |
| KC2 | Chlorophyll c2 | 263 |
| 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 | 250 |
| DD6 | (3S,3'R,5R,6S,7cis)-7',8'-didehydro-5,6-dihydro-5,6-epoxy-beta,beta-carotene-3,3'-diol | 244 |
| KC1 | Chlorophyll c1 | 184 |
| II0 | (1~{R})-3,5,5-trimethyl-4-[(3~{E},5~{E},7~{E},9~{E},11~{E},13~{E},15~{E})-3,7,12,16-tetramethyl-18-[(4~{R})-2,6,6-trimethyl-4-oxidanyl-cyclohexen-1-yl]octadeca-3,5,7,9,11,13,15-heptaen-1,17-diynyl]cyclohex-3-en-1-ol | 162 |
| SQD | 1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL | 147 |
| LMU | DODECYL-ALPHA-D-MALTOSIDE | 140 |
| DGD | DIGALACTOSYL DIACYL GLYCEROL (DGDG) | 121 |
| IHT | (1~{R})-3,5,5-trimethyl-4-[(3~{E},5~{E},7~{E},9~{E},11~{E},13~{E},15~{E},17~{E})-3,7,12,16-tetramethyl-18-(2,6,6-trimethylcyclohexen-1-yl)octadeca-3,5,7,9,11,13,15,17-octaen-1-ynyl]cyclohex-3-en-1-ol | 119 |
| 8CT | (6'R,11cis,11'cis,13cis,15cis)-4',5'-didehydro-5',6'-dihydro-beta,beta-carotene | 72 |
| 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 | 61 |
| UNL | Unknown ligand | 54 |