SARS-CoV-2 Ligands Database

RBD ACE

RBD (Receptor-Binding Domain) is a critical part of the coronavirus spike (S) protein, located within the S1 subunit. This domain is responsible for directly binding to the host cell receptor—such as ACE2 in the case of SARS-CoV-2—which is the key initial step for viral entry into the host cell.

The RBD undergoes conformational changes that regulate its accessibility to the receptor, switching between “up” (receptor-accessible) and “down” (receptor-inaccessible) states. Because of its essential role in viral attachment and entry, the RBD is a major target for neutralizing antibodies, vaccines, and therapeutic agents.

№	Extended PDB ID	PDB ID	Method	Resolution	Chain	Start	End	Macromolecules	Ligand 1	Ligand 2	Ligand 3	Ligand 4	Ligand 5
1	pdb_00006m0j	6M0J	X-ray	2.45 A	E	319	541	Spike protein S1	Angiotensin-converting enzyme 2	-	-	-	-
2	pdb_00006m17	6M17	EM	2.90 A	E/F	319	541	Spike protein S1	Sodium-dependent neutral amino acid transporter B(0)AT1	Angiotensin-converting enzyme 2	-	-	-
3	pdb_00007ekc	7EKC	X-ray	2.80 A	B	319	541	Spike protein S1	Angiotensin-converting enzyme 2	-	-	-	-
4	pdb_00007eke	7EKE	X-ray	2.70 A	B	319	541	Spike protein S1	Angiotensin-converting enzyme 2	-	-	-	-
5	pdb_00007ekf	7EKF	X-ray	2.85 A	B	319	541	Spike protein S1	Angiotensin-converting enzyme 2	-	-	-	-
6	pdb_00007ekg	7EKG	X-ray	2.63 A	B	319	541	Spike protein S1	Angiotensin-converting enzyme 2	-	-	-	-
7	pdb_00007ekh	7EKH	X-ray	2.40 A	B	319	541	Spike protein S1	Angiotensin-converting enzyme 2	-	-	-	-
8	pdb_00007sn0	7SN0	X-ray	3.08	C/D	319	541	Surface glycoprotein	Angiotensin-converting enzyme 2	-	-	-	-
9	pdb_00007w6u	7W6U	X-ray	2.56 A	B	319	541	Spike protein S1	Angiotensin-converting enzyme	-	-	-	-
10	pdb_00007w8s	7W8S	EM	2.85 A	B	319	541	Spike protein S1	Angiotensin-converting enzyme 2	-	-	-	-
11	pdb_00007wa1	7WA1	EM	2.90 A	B	319	541	Spike protein S1	Angiotensin-converting enzyme 2	-	-	-	-
12	pdb_00007wbp	7WBP	X-ray	3.00 A	B	319	541	Spike protein S1	Angiotensin-converting enzyme 2	-	-	-	-
13	pdb_00007wbq	7WBQ	X-ray	3.34 A	B/D	319	541	Spike protein S1	Angiotensin-converting enzyme 2	-	-	-	-
14	pdb_00007wnm	7WNM	X-ray	2.70 A	A	319	541	Spike protein S1	Angiotensin-converting enzyme 2	-	-	-	-
15	pdb_00007wsk	7WSK	X-ray	3.30 A	B	319	541	Spike protein S1	Processed angiotensin-converting enzyme 2	-	-	-	-
16	pdb_00007xa7	7XA7	X-ray	3.31 A	B/D/F/H	319	541	Spike protein S1	Angiotensin-converting enzyme	-	-	-	-
17	pdb_00007xby	7XBY	X-ray	2.85 A	B	319	541	Spike protein S1	Angiotensin-converting enzyme	-	-	-	-
18	pdb_00007y75	7Y75	EM	3.10 A	E/F	319	541	Spike protein S1	Sodium- and chloride-dependent transporter XTRP3	Angiotensin-converting enzyme 2	-	-	-
19	pdb_00007y76	7Y76	EM	3.20 A	E/F	319	541	Spike protein S1	SIT1	Angiotensin-converting enzyme 2	-	-	-
20	pdb_00007zdq	7ZDQ	EM	3.20 A	B	319	541	Spike protein S1	Processed angiotensin-converting enzyme 2	-	-	-	-
21	pdb_00008i9e	8I9E	EM	3.20 A	E	319	541	Spike protein S1	Processed angiotensin-converting enzyme 2	-	-	-	-
22	pdb_00008i9f	8I9F	EM	2.90 A	E	319	541	Spike protein S2'	Processed angiotensin-converting enzyme 2	-	-	-	-
23	pdb_00008i9g	8I9G	EM	3.20 A	A	319	541	Spike protein S2'	Processed angiotensin-converting enzyme 2	-	-	-	-
24	pdb_00008i9h	8I9H	EM	3.60 A	E	319	541	Spike protein S2'	Processed angiotensin-converting enzyme 2	-	-	-	-
25	pdb_00008ifz	8IFZ	EM	2.85 A	B	319	541	Spike protein S1	Angiotensin-converting enzyme	-	-	-	-
26	pdb_00008wdr	8WDR	X-ray	3.47 A	B/D	319	541	Spike protein S1	Angiotensin-converting enzyme 2	-	-	-	-
27	pdb_00008wds	8WDS	X-ray	3.40 A	B/D	319	541	Spike protein S1	Angiotensin-converting enzyme 2	-	-	-	-
28	pdb_00008wdy	8WDY	EM	2.69 A	B	319	541	Spike protein S1	Angiotensin-converting enzyme 2	-	-	-	-
29	pdb_00008we0	8WE0	EM	2.80 A	B	319	541	Spike protein S2'	Angiotensin-converting enzyme 2	-	-	-	-
30	pdb_00008we1	8WE1	EM	2.47 A	B	319	541	Spike protein S2'	Angiotensin-converting enzyme 2	-	-	-	-
31	pdb_00008we4	8WE4	EM	2.91 A	B	319	541	Spike protein S1	Angiotensin-converting enzyme 2	S304 Fab Heavy Chain	S304 Fab Light Chain	-	-
32	pdb_00008wox	8WOX	EM	2.75 A	B	319	541	Spike protein S1	Angiotensin-converting enzyme	-	-	-	-
33	pdb_00008wp8	8WP8	EM	2.89 A	B	319	541	Spike protein S1	Processed angiotensin-converting enzyme 2	-	-	-	-
34	pdb_00008xn2	8XN2	EM	2.79 A	B	319	541	Spike protein S1	Angiotensin-converting enzyme 2	-	-	-	-
35	pdb_00008xn3	8XN3	EM	2.64 A	B	319	541	Spike protein S1	Angiotensin-converting enzyme 2	-	-	-	-
36	pdb_0000 8xsj	8XSJ	EM	2.64 A	B	319	541	Spike protein S1	Angiotensin-converting enzyme 2	IMCAS-316 H chain	IMCAS-316 L chain	-	-
37	pdb_00008xzd	8XZD	EM	3.47 A	B	319	541	Spike protein S1	Angiotensin-converting enzyme	-	-	-	-
38	pdb_00008y6a	8Y6A	EM	2.72 A	B	319	541	Spike protein S1	Angiotensin-converting enzyme 2	Heavy chain of S309 Fab	Light chain of S309 Fab	-	-
39	pdb_00008wdz	8WDZ	EM	2.71 A	B	319	541	Spike protein S1	Angiotensin-converting enzyme 2	-	-	-	-
40	pdb_00008woy	8WOY	EM	3.14 A	B	319	541	Spike protein S1	Angiotensin-converting enzyme	-	-	-	-
41	pdb_00008vqr	8VQR	X-ray	2.56 A	E/F	319	536	Spike protein S1	Angiotensin-converting enzyme, Processed angiotensin-converting enzyme 2	-	-	-	-
42	pdb_00007ufk	7UFK	X-ray	2.38 A	E/F	319	535	Spike protein S1	Angiotensin-converting enzyme 2	-	-	-	-
43	pdb_00007ufl	7UFL	X-ray	2.84 A	E/F	319	535	Spike protein S1	Angiotensin-converting enzyme 2	-	-	-	-
44	pdb_00007dmu	7DMU	X-ray	3.20 A	B/D	319	531	Spike protein S1	Angiotensin-converting enzyme 2	-	-	-	-
45	pdb_00006lzg	6LZG	X-ray	2.50 A	B	319	527	Spike protein S1	Angiotensin-converting enzyme 2	-	-	-	-
46	pdb_00008xsf	8XSF	EM	2.16 A	B	319	527	Spike protein S1	Angiotensin-converting enzyme 2	IMCAS-364 H chain	IMCAS-364 L chain	-	-
47	pdb_00007efp	7EFP	X-ray	2.70 A	B	320	537	Spike glycoprotein	Processed angiotensin-converting enzyme 2	-	-	-	-
48	pdb_00007rpv	7RPV	X-ray	3.54 A	E/F/G/H	320	537	Spike protein S1	Processed angiotensin-converting enzyme 2	-	-	-	-
49	pdb_00007efr	7EFR	X-ray	2.49 A	B	321	537	Spike glycoprotein	Processed angiotensin-converting enzyme 2	-	-	-	-
50	pdb_00008t23	8T23	EM	3.87 A	B	321	528	Spike glycoprotein	Angiotensin-converting enzyme	-	-	-	-
51	pdb_00008t25	8T25	EM	3.62 A	B	321	528	Spike glycoprotein	Angiotensin-converting enzyme	-	-	-	-
52	pdb_00007xwa	7XWA	X-ray	3.36 A	B/D	322	536	Spike protein S1	Processed angiotensin-converting enzyme 2	-	-	-	-
53	pdb_00008if2	8IF2	X-ray	2.78 A	B	322	536	Spike protein S1	Processed angiotensin-converting enzyme 2	-	-	-	-
54	pdb_00008xyz	8XYZ	EM	2.96 A	B	323	541	Signal peptide, Spike protein S1	Angiotensin-converting enzyme	-	-	-	-
55	pdb_00007l7f	7L7F	EM	3.24 A	E/F	323	528	Spike glycoprotein, Envelope glycoprotein fusion	Angiotensin-converting enzyme 2	-	-	-	-
56	pdb_00007tn0	7TN0	X-ray	2.85 A	I/S	324	531	Spike protein S1	S309 light chain	S309 heavy chain	Angiotensin-converting enzyme 2	S304 Fab light chain	S304 Fab heavy chain
57	pdb_00007l0n	7L0N	X-ray	2.78 A	R/S	328	531	Spike protein S1	Monoclonal antibody S309 Fab light chain	Monoclonal antibody S309 Fab heavy chain	Monoclonal antibody S304 Fab light chain	Monoclonal antibody S304 Fab heavy chain	Angiotensin-converting enzyme 2
58	pdb_00008df5	8DF5	X-ray	2.70 A	R/S	328	529	Spike protein S1	S309 Fab Heavy Chain	S309 Fab Light Chain	Angiotensin-converting enzyme 2	S304 Fab Heavy Chain	S304 Fab Light Chain
59	pdb_00008s9g	8S9G	EM	3.00 A	E	328	529	Spike glycoprotein	Processed angiotensin-converting enzyme 2	S309 Fab Heavy chain	S309 Fab Light chain	-	-
60	pdb_00008fxb	8FXB	EM	3.10 A	E	328	528	Spike protein S1	S309 Light chain	S309 Heavy chain	Processed angiotensin-converting enzyme 2	-	-
61	pdb_00008fxc	8FXC	EM	3.20 A	E	328	528	Spike protein S1	S309 Light chain	S309 Heavy chain	Processed angiotensin-converting enzyme 2	-	-
62	pdb_00007zf7	7ZF7	X-ray	3.46 A	B	330	532	Spike protein S1	Processed angiotensin-converting enzyme 2	-	-	-	-
63	pdb_00007wsa	7WSA	EM	3.00 A	A	330	530	Spike protein S1	Processed angiotensin-converting enzyme 2	-	-	-	-
64	pdb_00008vkn	8VKN	EM	2.93 A	A	330	527	Spike protein S1	Angiotensin-converting enzyme 2	-	-	-	-
65	pdb_00008vkp	8VKP	EM	2.77 A	A	330	527	Spike protein S1	Processed angiotensin-converting enzyme 2	-	-	-	-
66	pdb_00007yv8	7YV8	X-ray	2.94 A	E	332	528	BANAL 236 coronavirus spike receptor-binding domain	Processed angiotensin-converting enzyme 2	-	-	-	-
67	pdb_00007yv8	7YV8	EM	2.94 A	B	332	528	Spike glycoprotein	Angiotensin-converting enzyme	-	-	-	-
68	pdb_00008qsq	8QSQ	EM	3.70 A	A	332	527	Spike protein S2'	Processed angiotensin-converting enzyme 2	-	-	-	-
69	pdb_00007lo4	7LO4	X-ray	2.46 A	B	333	530	Spike protein S1	Processed angiotensin-converting enzyme 2	-	-	-	-
70	pdb_00007fc5	7FC5	X-ray	2.89 A	E	333	529	Spike protein S1	Angiotensin-converting enzyme	-	-	-	-
71	pdb_00007bh9	7BH9	EM	2.90 A	E	333	528	Spike protein S1	Angiotensin-converting enzyme 2	-	-	-	-
72	pdb_00007nxc	7NXC	X-ray	3.14 A	B	333	528	Spike protein S1	Processed angiotensin-converting enzyme 2	-	-	-	-
73	pdb_00007c8d	7C8D	EM	3.00 A	B	333	527	Spike protein S1	Angiotensin-converting enzyme 2	-	-	-	-
74	pdb_00007c8j	7C8J	X-ray	3.18 A	B	333	527	SARS-CoV-2 Receptor binding domain	Angiotensin-converting enzyme	-	-	-	-
75	pdb_00007wbl	7WBL	EM	3.40 A	B	333	527	Spike protein S1	Angiotensin-converting enzyme 2	-	-	-	-
76	pdb_00007wse	7WSE	EM	2.93 A	B	333	527	Spike protein S1	Angiotensin-converting enzyme	-	-	-	-
77	pdb_00007wsh	7WSH	EM	2.83 A	B	333	527	Spike protein S1	Angiotensin-converting enzyme	-	-	-	-
78	pdb_00007xaz	7XAZ	X-ray	3.00 A	B/D	333	527	Spike protein S1	Angiotensin-converting enzyme 2	-	-	-	-
79	pdb_00007xb0	7XB0	X-ray	2.90 A	B	333	527	Spike protein S1	Angiotensin-converting enzyme 2	-	-	-	-
80	pdb_00007xb1	7XB1	X-ray	2.70 A	B	333	527	Spike protein S1	Angiotensin-converting enzyme 2	-	-	-	-
81	pdb_00007xci	7XCI	EM	3.20 A	B	333	527	Spike glycoprotein	Processed angiotensin-converting enzyme 2	-	-	-	-
82	pdb_00007xcp	7XCP	EM	3.05 A	B	333	527	Spike protein S1	Processed angiotensin-converting enzyme 2	Heavy chain of 304 Fab	Lignt chain of 304 Fab	-	-
83	pdb_00007ya1	7YA1	EM	3.11 A	B	333	527	Spike protein S1	Angiotensin-converting enzyme 2	-	-	-	-
84	pdb_00007yhw	7YHW	EM	3.09 A	B	333	527	Spike protein S1	Angiotensin-converting enzyme 2	-	-	-	-
85	pdb_00007yj3	7YJ3	EM	3.14 A	B	333	527	Spike protein S1	Angiotensin-converting enzyme 2	-	-	-	-
86	pdb_00007yvu	7YVU	EM	3.20 A	B	333	527	Spike protein S1	Processed angiotensin-converting enzyme 2	-	-	-	-
87	pdb_00008gry	8GRY	EM	3.29	B	333	527	Spike protein S1	Processed angiotensin-converting enzyme 2	-	-	-	-
88	pdb_00008h06	8H06	EM	2.66	B	333	527	Spike protein S1	Processed angiotensin-converting enzyme 2	-	-	-	-
89	pdb_00008h5c	8H5C	X-ray	2.90	B	333	527	Spike protein S1	Processed angiotensin-converting enzyme 2	-	-	-	-
90	pdb_00008hg0	8HG0	EM	3.51	B	333	527	Spike protein S1	Angiotensin-converting enzyme	-	-	-	-
91	pdb_00008whz	8WHZ	EM	3.93	B	333	527	Spike protein S1	Processed angiotensin-converting enzyme 2	-	-	-	-
92	pdb_00007dqa	7DQA	EM	2.80	C	333	526	Spike glycoprotein	Angiotensin-converting enzyme 2	-	-	-	-
93	pdb_00007dx4	7DX4	EM	3.60	E	333	526	Spike protein S1	Angiotensin-converting enzyme 2	Heavy chain of FC08 Fab	Light chain of FC08 Fab	-	-
94	pdb_00007fdh	7FDH	EM	4.20 A	A	333	526	Spike protein S1	Angiotensin-converting enzyme 2	-	-	-	-
95	pdb_00007fdg	7FDG	EM	4.20 A	A	333	526	Spike protein S1	Angiotensin-converting enzyme 2	-	-	-	-
96	pdb_00007fdi	7FDI	X-ray	2.90 A	C	333	526	Spike protein S1	Angiotensin-converting enzyme 2	-	-	-	-
97	pdb_00007fdk	7FDK	X-ray	3.14 A	C/F/I/L	333	526	Spike protein S1	Angiotensin-converting enzyme 2	-	-	-	-
98	pdb_00007w9i	7W9I	X-ray	1.82 A	E	333	526	Spike protein S1	Angiotensin-converting enzyme 2	-	-	-	-
99	pdb_00007whh	7WHH	X-ray	3.65 A	E	333	526	Spike glycoprotein	Processed angiotensin-converting enzyme 2	-	-	-	-
100	pdb_00008asy	8ASY	X-ray	4.24 A	A/B/C/D	333	526	Spike protein S1	Processed angiotensin-converting enzyme 2	-	-	-	-
101	pdb_00008hfy	8HFY	X-ray	3.29 A	E	333	526	Spike protein S1	Angiotensin-converting enzyme	-	-	-	-
102	pdb_00008hrk	8HRK	X-ray	2.60 A	E	333	526	Spike protein S1	Processed angiotensin-converting enzyme 2	-	-	-	-
103	pdb_00008hrl	8HRL	X-ray	2.00 A	A	333	526	Spike protein S1	Processed angiotensin-converting enzyme 2	-	-	-	-
104	pdb_00008ka8	8KA8	EM	3.16 A	A	333	526	Spike protein S1	Angiotensin-converting enzyme	-	-	-	-
105	pdb_00008kc2	8KC2	EM	3.21 A	B	333	526	Spike protein S1	Angiotensin-converting enzyme	-	-	-	-
106	pdb_00007p19	7P19	EM	3.81 A	F	333	521	Spike protein S1	Processed angiotensin-converting enzyme 2	-	-	-	-
107	pdb_00008wtd	8WTD	EM	3.16 A	A	333	520	Spike protein S2'	Angiotensin-converting enzyme 2	-	-	-	-
108	pdb_00008wrh	8WRH	X-ray	2.50 A	B/D	334	530	Spike protein S2'	Angiotensin-converting enzyme 2	-	-	-	-
109	pdb_00008wrl	8WRL	X-ray	2.20 A	A/C	334	530	Spike protein S1	Processed angiotensin-converting enzyme 2	-	-	-	-
110	pdb_00007yr4	7YR4	EM	4.10 A	A	334	528	Spike glycoprotein	Angiotensin-converting enzyme 2	-	-	-	-
111	pdb_00007ydi	7YDI	EM	3.50 A	R	334	526	Spike protein S1	Processed angiotensin-converting enzyme 2	Heavy chain of R1-32	Light chain of R1-32	-	-
112	pdb_00008xxw	8XXW	EM	3.42 A	R	335	526	Spike protein S1	Processed angiotensin-converting enzyme 2	M2-7-Heavy chain	M2-7-Light chain	-	-
113	pdb_00006vw1	6VW1	X-ray	1.63 A	C	418	425	SARS-CoV-2 chimeric RBD	Angiotensin-converting enzyme 2	-	-	-	-