ECOD
X-group (possible homology)

4169 Coronavirus spike protein receptor-binding domain

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Ligands and drugs

5,131
Member domains
3,174
with ligand contacts (≤ 4 Å)
61.9% of members
1,568
with DrugDomain annotations
30.6% of members
1,543
with a DrugBank compound
30.1% 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.

51
Proteins with classified ligands
7
Superclasses bound (of 23)
4.6
Superclasses per 20 proteins
narrower than 87% 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.

SuperclassProteinsExpected
0.25×observed / expected4×
RatioSignificance
Organic oxygen compounds5010.04.99×q < 0.0001
Lipids and lipid-like molecules45.60.71×q = 0.73
Homogeneous non-metal compounds410.80.37×q = 0.03
Organic acids and derivatives17.80.13×q = 0.01
Organoheterocyclic compounds17.70.13×q = 0.01
Homogeneous metal compounds224.70.08×q < 0.0001
Nucleosides, nucleotides, and analogues013.90q < 0.0001
Organosulfur compounds11.00.97×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

DrugBankPDB ligandNameDomains
DB00141NAGN-Acetylglucosamine1,452
DB14104EICLinoleic acid72
DB04224ELAOleic Acid6
DB00755REATretinoin3
DB03193STEStearic acid3
DB03796PLMPalmitic Acid3
DB00142GLUGlutamic acid2
DB00172PROProline2
DB03740NDGN-acetyl-alpha-D-glucosamine2
DB04473FUCalpha-L-fucose2
DB03175POLPropyl alcohol1

Most frequently bound compounds

PDB ligandNameDomains in contact
NAG2-acetamido-2-deoxy-beta-D-glucopyranose3,041
EICLINOLEIC ACID102
CLCHLORIDE ION34
8Z9Sapienic acid19
PLMPALMITIC ACID9
STESTEARIC ACID9
KZ02,4,6-tris(chloromethyl)-1,3,5-triazine7
ELAElaidic acid6
IDU2-O-sulfo-beta-L-altropyranuronic acid3
NAmetalSODIUM ION3
OLAOLEIC ACID3
PG02-(2-METHOXYETHOXY)ETHANOL3
PROPROLINE3
Q837-(6-nitro-2,3-dihydroindol-1-yl)-7-oxidanylidene-heptanoic acid3
REARETINOIC ACID3
VCG2-hydroxyethyl 2-deoxy-3,5-bis-O-(2-hydroxyethyl)-6-O-(2-{[(9E)-octadec-9-enoyl]oxy}ethyl)-alpha-L-xylo-hexofuranoside3
MGmetalMAGNESIUM ION2
NDG2-acetamido-2-deoxy-alpha-D-glucopyranose2
P4G1-ETHOXY-2-(2-ETHOXYETHOXY)ETHANE2
XIO[(2~{S})-2-[[4-(2-azanylethanoylamino)-7-[[(2~{S})-3-[2-(4-nitrophenyl)sulfanyl-1~{H}-indol-3-yl]-1-oxidanylidene-1-sodiooxy-propan-2-yl]amino]-4-[3-[[(2~{S})-3-[2-(4-nitrophenyl)sulfanyl-1~{H}-indol-3-yl]-1-oxidanylidene-1-sodiooxy-propan-2-yl]amino]-3-oxidanylidene-propyl]-7-oxidanylidene-heptanoyl]amino]-3-[2-(4-nitrophenyl)sulfanyl-1~{H}-indol-3-yl]propanoyl]oxysodium2