Receptor
PDB id Resolution Class Description Source Keywords
5O1B 1.43 Å NON-ENZYME: BINDING P53 CANCER MUTANT Y220C IN COMPLEX WITH COMPOUND MB84 HOMO SAPIENS P53 TUMOR SUPPRESSOR CANCER MUTATION PROTEIN STABILIZATIOMOLECULE STABILIZERS CANCER THERAPY DNA BINDING PROTEIN CHAPERONES
Ref.: AMINOBENZOTHIAZOLE DERIVATIVES STABILIZE THE THERMO P53 CANCER MUTANT Y220C AND SHOW ANTICANCER ACTIVIT P53-Y220C CELL LINES. EUR J MED CHEM V. 152 101 2018
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
ZN B:401;
A:401;
 Part of Protein;
Part of Protein;
 none;
none;
 submit data
65.409 Zn [Zn+2...
GOL B:403;
B:404;
A:403;
A:404;
 Invalid;
Invalid;
Invalid;
Invalid;
 none;
none;
none;
none;
 submit data
92.094 C3 H8 O3 C(C(C...
9H2 B:402;
A:402;
 Valid;
Valid;
 none;
none;
 Kd = 20 uM
441.004 C11 H9 I2 N O2 c1ccn...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
6SI3 1.4 Å NON-ENZYME: BINDING P53 CANCER MUTANT Y220S IN COMPLEX WITH SMALL-MOLECULE STABI PK9301 HOMO SAPIENS P53 TRANSCRIPTION FACTOR TUMOR SUPPRESSOR CANCER THERAPYONCOGENIC MUTANT PROTEIN MISFOLDING DNA-BINDING DOMAIN DSURFACE CREVICE SMALL-MOLECULE STABILIZER MUTANT P53 RESCBINDING PROTEIN
Ref.: TARGETING CAVITY-CREATING P53 CANCER MUTATIONS WITH SMALL-MOLECULE STABILIZERS: THE Y220X PARADIGM. ACS CHEM.BIOL. V. 15 657 2020
Members (40)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 552 families.
1 2X0W - X0W C10 H11 N O2 S Cc1nc2cc(c....
2 4AGM Kd = 105 uM P86 C16 H24 I2 N2 O CCN(CC)C1C....
3 5AB9 Kd = 470 uM 92O C15 H20 N2 CCc1cccc2c....
4 6GGE - EYE C21 H23 N2 S CCn1c2ccc(....
5 2X0V - X0V C7 H7 F3 N2 c1cc(c(cc1....
6 5O1A Kd = 30 uM 9H5 C16 H17 I2 N3 O2 CN1CCN(CC1....
7 5G4O Kd = 37.2 uM O80 C17 H17 F3 N2 CN(C)Cc1cc....
8 5O1F Kd = 30 uM 9GQ C15 H16 I N O4 CCCCOc1cc(....
9 5AOJ Kd = 21 uM Y0V C11 H7 I2 N O3 c1ccn(c1)c....
10 6GGF - EXQ C21 H23 N2 S CCn1c2ccc(....
11 5O1G Kd = 116 uM 9GK C19 H16 I N O4 c1ccc(cc1)....
12 5O1I Kd = 4 uM 9GH C16 H16 I N3 O3 S CCN(CC)c1n....
13 5AOL Kd = 4800 uM UFV C7 H6 Br F3 N2 c1c(cc(c(c....
14 6GGC - EXN C20 H21 N2 O CCn1c2ccc(....
15 5AOI Kd = 940 uM RZH C13 H17 Br N2 CCc1cc(cc2....
16 5O1D Kd = 22 uM 9GW C14 H14 I N O4 CCCOc1cc(c....
17 4AGP Kd = 20.6 uM P51 C25 H31 I N2 O2 CCN(CC)C1C....
18 6SI4 Kd = 5.9 uM LEK C19 H19 N3 S CCn1c2ccc(....
19 3ZME - QC5 C17 H19 F N4 CN(C)CCn1c....
20 5AOK - GOH C11 H10 N6 O c1ccn(c1)c....
21 6SI3 Kd = 4 uM LEB C16 H14 Br F3 N2 CNCc1ccc2c....
22 5A7B Kd = 271 uM KMN C27 H32 N2 O2 CCN(CC)C1C....
23 5ABA Kd = 1040 uM UL7 C17 H24 Br Cl N2 O2 c1c(cc(c(c....
24 6GGD - EYB C19 H20 N3 O CCn1c2ccc(....
25 2VUK Kd = 125 uM P83 C16 H18 N2 CCn1c2cccc....
26 4AGQ Kd = 9.7 uM P96 C25 H32 I N3 O CCN(CC)C1C....
27 5O1E Kd = 33 uM 9GT C14 H12 I N O4 C=CCOc1cc(....
28 4AGN Kd = 107 uM NXG C19 H27 I N2 O2 CCN(CC)C1C....
29 6GGA - EY2 C16 H18 Br N2 CCn1c2ccc(....
30 5O1B Kd = 20 uM 9H2 C11 H9 I2 N O2 c1ccn(c1)c....
31 5AOM Kd = 1270 uM FY8 C12 H15 Cl N2 O2 c1cc(c(cc1....
32 2X0U - X0U C9 H8 N2 O2 S c1c2c(cc3c....
33 4AGO Kd = 15.5 uM P74 C24 H36 I N3 O3 CCN(CC)C1C....
34 5O1C Kd = 113 uM 9GZ C17 H11 F I N O3 c1ccn(c1)c....
35 5G4N Kd = 101 uM O83 C16 H16 F2 N2 CNCc1ccc2c....
36 6GGB - EXQ C21 H23 N2 S CCn1c2ccc(....
37 5O1H Kd = 14 uM 9GN C14 H14 I N O3 S CCCSc1cc(c....
38 4AGL Kd = 225 uM P84 C14 H20 I2 N2 O CN1CCC(CC1....
39 6SI0 Kd = 5.3 uM LEK C19 H19 N3 S CCn1c2ccc(....
40 5G4M Kd = 138 uM O82 C16 H17 F N2 CNCc1ccc2c....
70% Homology Family (40)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 426 families.
1 2X0W - X0W C10 H11 N O2 S Cc1nc2cc(c....
2 4AGM Kd = 105 uM P86 C16 H24 I2 N2 O CCN(CC)C1C....
3 5AB9 Kd = 470 uM 92O C15 H20 N2 CCc1cccc2c....
4 6GGE - EYE C21 H23 N2 S CCn1c2ccc(....
5 2X0V - X0V C7 H7 F3 N2 c1cc(c(cc1....
6 5O1A Kd = 30 uM 9H5 C16 H17 I2 N3 O2 CN1CCN(CC1....
7 5G4O Kd = 37.2 uM O80 C17 H17 F3 N2 CN(C)Cc1cc....
8 5O1F Kd = 30 uM 9GQ C15 H16 I N O4 CCCCOc1cc(....
9 5AOJ Kd = 21 uM Y0V C11 H7 I2 N O3 c1ccn(c1)c....
10 6GGF - EXQ C21 H23 N2 S CCn1c2ccc(....
11 5O1G Kd = 116 uM 9GK C19 H16 I N O4 c1ccc(cc1)....
12 5O1I Kd = 4 uM 9GH C16 H16 I N3 O3 S CCN(CC)c1n....
13 5AOL Kd = 4800 uM UFV C7 H6 Br F3 N2 c1c(cc(c(c....
14 6GGC - EXN C20 H21 N2 O CCn1c2ccc(....
15 5AOI Kd = 940 uM RZH C13 H17 Br N2 CCc1cc(cc2....
16 5O1D Kd = 22 uM 9GW C14 H14 I N O4 CCCOc1cc(c....
17 4AGP Kd = 20.6 uM P51 C25 H31 I N2 O2 CCN(CC)C1C....
18 6SI4 Kd = 5.9 uM LEK C19 H19 N3 S CCn1c2ccc(....
19 3ZME - QC5 C17 H19 F N4 CN(C)CCn1c....
20 5AOK - GOH C11 H10 N6 O c1ccn(c1)c....
21 6SI3 Kd = 4 uM LEB C16 H14 Br F3 N2 CNCc1ccc2c....
22 5A7B Kd = 271 uM KMN C27 H32 N2 O2 CCN(CC)C1C....
23 5ABA Kd = 1040 uM UL7 C17 H24 Br Cl N2 O2 c1c(cc(c(c....
24 6GGD - EYB C19 H20 N3 O CCn1c2ccc(....
25 2VUK Kd = 125 uM P83 C16 H18 N2 CCn1c2cccc....
26 4AGQ Kd = 9.7 uM P96 C25 H32 I N3 O CCN(CC)C1C....
27 5O1E Kd = 33 uM 9GT C14 H12 I N O4 C=CCOc1cc(....
28 4AGN Kd = 107 uM NXG C19 H27 I N2 O2 CCN(CC)C1C....
29 6GGA - EY2 C16 H18 Br N2 CCn1c2ccc(....
30 5O1B Kd = 20 uM 9H2 C11 H9 I2 N O2 c1ccn(c1)c....
31 5AOM Kd = 1270 uM FY8 C12 H15 Cl N2 O2 c1cc(c(cc1....
32 2X0U - X0U C9 H8 N2 O2 S c1c2c(cc3c....
33 4AGO Kd = 15.5 uM P74 C24 H36 I N3 O3 CCN(CC)C1C....
34 5O1C Kd = 113 uM 9GZ C17 H11 F I N O3 c1ccn(c1)c....
35 5G4N Kd = 101 uM O83 C16 H16 F2 N2 CNCc1ccc2c....
36 6GGB - EXQ C21 H23 N2 S CCn1c2ccc(....
37 5O1H Kd = 14 uM 9GN C14 H14 I N O3 S CCCSc1cc(c....
38 4AGL Kd = 225 uM P84 C14 H20 I2 N2 O CN1CCC(CC1....
39 6SI0 Kd = 5.3 uM LEK C19 H19 N3 S CCn1c2ccc(....
40 5G4M Kd = 138 uM O82 C16 H17 F N2 CNCc1ccc2c....
50% Homology Family (40)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 322 families.
1 2X0W - X0W C10 H11 N O2 S Cc1nc2cc(c....
2 4AGM Kd = 105 uM P86 C16 H24 I2 N2 O CCN(CC)C1C....
3 5AB9 Kd = 470 uM 92O C15 H20 N2 CCc1cccc2c....
4 6GGE - EYE C21 H23 N2 S CCn1c2ccc(....
5 2X0V - X0V C7 H7 F3 N2 c1cc(c(cc1....
6 5O1A Kd = 30 uM 9H5 C16 H17 I2 N3 O2 CN1CCN(CC1....
7 5G4O Kd = 37.2 uM O80 C17 H17 F3 N2 CN(C)Cc1cc....
8 5O1F Kd = 30 uM 9GQ C15 H16 I N O4 CCCCOc1cc(....
9 5AOJ Kd = 21 uM Y0V C11 H7 I2 N O3 c1ccn(c1)c....
10 6GGF - EXQ C21 H23 N2 S CCn1c2ccc(....
11 5O1G Kd = 116 uM 9GK C19 H16 I N O4 c1ccc(cc1)....
12 5O1I Kd = 4 uM 9GH C16 H16 I N3 O3 S CCN(CC)c1n....
13 5AOL Kd = 4800 uM UFV C7 H6 Br F3 N2 c1c(cc(c(c....
14 6GGC - EXN C20 H21 N2 O CCn1c2ccc(....
15 5AOI Kd = 940 uM RZH C13 H17 Br N2 CCc1cc(cc2....
16 5O1D Kd = 22 uM 9GW C14 H14 I N O4 CCCOc1cc(c....
17 4AGP Kd = 20.6 uM P51 C25 H31 I N2 O2 CCN(CC)C1C....
18 6SI4 Kd = 5.9 uM LEK C19 H19 N3 S CCn1c2ccc(....
19 3ZME - QC5 C17 H19 F N4 CN(C)CCn1c....
20 5AOK - GOH C11 H10 N6 O c1ccn(c1)c....
21 6SI3 Kd = 4 uM LEB C16 H14 Br F3 N2 CNCc1ccc2c....
22 5A7B Kd = 271 uM KMN C27 H32 N2 O2 CCN(CC)C1C....
23 5ABA Kd = 1040 uM UL7 C17 H24 Br Cl N2 O2 c1c(cc(c(c....
24 6GGD - EYB C19 H20 N3 O CCn1c2ccc(....
25 2VUK Kd = 125 uM P83 C16 H18 N2 CCn1c2cccc....
26 4AGQ Kd = 9.7 uM P96 C25 H32 I N3 O CCN(CC)C1C....
27 5O1E Kd = 33 uM 9GT C14 H12 I N O4 C=CCOc1cc(....
28 4AGN Kd = 107 uM NXG C19 H27 I N2 O2 CCN(CC)C1C....
29 6GGA - EY2 C16 H18 Br N2 CCn1c2ccc(....
30 5O1B Kd = 20 uM 9H2 C11 H9 I2 N O2 c1ccn(c1)c....
31 5AOM Kd = 1270 uM FY8 C12 H15 Cl N2 O2 c1cc(c(cc1....
32 2X0U - X0U C9 H8 N2 O2 S c1c2c(cc3c....
33 4AGO Kd = 15.5 uM P74 C24 H36 I N3 O3 CCN(CC)C1C....
34 5O1C Kd = 113 uM 9GZ C17 H11 F I N O3 c1ccn(c1)c....
35 5G4N Kd = 101 uM O83 C16 H16 F2 N2 CNCc1ccc2c....
36 6GGB - EXQ C21 H23 N2 S CCn1c2ccc(....
37 5O1H Kd = 14 uM 9GN C14 H14 I N O3 S CCCSc1cc(c....
38 4AGL Kd = 225 uM P84 C14 H20 I2 N2 O CN1CCC(CC1....
39 6SI0 Kd = 5.3 uM LEK C19 H19 N3 S CCn1c2ccc(....
40 5G4M Kd = 138 uM O82 C16 H17 F N2 CNCc1ccc2c....
Polypharmacology
Similar Ligands (2D)
Ligand no: 1; Ligand: 9H2; Similar ligands found: 2
No: Ligand ECFP6 Tc MDL keys Tc
1 9H2 1 1
2 Y0V 0.461538 0.833333
Similar Ligands (3D)
Ligand no: 1; Ligand: 9H2; Similar ligands found: 204
No: Ligand Similarity coefficient
1 NDG 0.9613
2 NAG 0.9576
3 GDL 0.9521
4 AU8 0.9491
5 LOG 0.9463
6 MAG 0.9453
7 NOK 0.9363
8 SNG 0.9355
9 BNX 0.9339
10 S0G 0.9294
11 MQG 0.9244
12 NGA 0.9227
13 BGN 0.9184
14 OQC 0.9180
15 CP7 0.9165
16 3R4 0.9120
17 GF4 0.9112
18 54E 0.9110
19 89J 0.9110
20 EV2 0.9102
21 0OK 0.9080
22 KF5 0.9069
23 A2G 0.9069
24 9KZ 0.9041
25 68A 0.9030
26 A4N 0.9024
27 0J4 0.9020
28 KMY 0.9008
29 DC5 0.9008
30 F4K 0.9007
31 DJN 0.8999
32 MIL 0.8996
33 363 0.8990
34 9FH 0.8980
35 92O 0.8957
36 RKN 0.8950
37 CC5 0.8946
38 27B 0.8939
39 L1O 0.8937
40 X48 0.8933
41 2F8 0.8927
42 CP6 0.8914
43 KP2 0.8910
44 2CZ 0.8907
45 LP8 0.8906
46 22L 0.8897
47 C1M 0.8895
48 CPZ 0.8893
49 1BW 0.8892
50 BBK 0.8888
51 TR4 0.8881
52 977 0.8877
53 FYR 0.8874
54 GJP 0.8872
55 9GW 0.8864
56 RVE 0.8863
57 MUR 0.8858
58 HBI 0.8857
59 H2B 0.8857
60 BPY 0.8856
61 AUT 0.8856
62 CFA 0.8855
63 428 0.8853
64 LNR 0.8847
65 H4B 0.8846
66 4AB 0.8846
67 BM3 0.8846
68 1A5 0.8845
69 3N1 0.8845
70 BIO 0.8840
71 6E8 0.8835
72 1CY 0.8834
73 8NX 0.8832
74 IAC 0.8823
75 9GN 0.8817
76 9GT 0.8815
77 S0E 0.8815
78 AWE 0.8813
79 FMQ 0.8813
80 FF2 0.8809
81 A9K 0.8808
82 I4D 0.8808
83 42R 0.8804
84 A4T 0.8800
85 BA5 0.8799
86 3XR 0.8791
87 K68 0.8789
88 DHC 0.8788
89 N3W 0.8784
90 86L 0.8774
91 PMP 0.8771
92 S3C 0.8770
93 TYR 0.8770
94 PLP 0.8764
95 JYT 0.8763
96 GC2 0.8760
97 2P3 0.8760
98 C2M 0.8760
99 JO5 0.8758
100 ALX 0.8755
101 VC3 0.8751
102 5NS 0.8743
103 2JX 0.8743
104 OA4 0.8741
105 MSR 0.8732
106 F5F 0.8730
107 54Z 0.8725
108 ZEC 0.8724
109 K3Q 0.8724
110 MPK 0.8723
111 DAH 0.8722
112 PH2 0.8717
113 6J5 0.8715
114 8NB 0.8711
115 OX2 0.8711
116 AMR 0.8709
117 X04 0.8709
118 FCW 0.8708
119 F5C 0.8701
120 SNU 0.8697
121 5AD 0.8695
122 JXK 0.8694
123 K82 0.8686
124 NBG 0.8686
125 6HP 0.8686
126 EXD 0.8684
127 5GT 0.8683
128 BHQ 0.8680
129 HHR 0.8679
130 KGK 0.8677
131 TRP 0.8676
132 2K8 0.8675
133 NPS 0.8671
134 CLU 0.8670
135 LZB 0.8669
136 QME 0.8668
137 9R5 0.8662
138 MMS 0.8659
139 BHS 0.8658
140 QIV 0.8658
141 PQS 0.8657
142 2O6 0.8657
143 A4Q 0.8657
144 4I8 0.8657
145 H75 0.8654
146 MNS 0.8652
147 HNH 0.8649
148 3C4 0.8648
149 7EH 0.8647
150 CR1 0.8646
151 4GP 0.8646
152 BY5 0.8645
153 KY3 0.8644
154 657 0.8643
155 3QI 0.8639
156 IPD 0.8635
157 GZQ 0.8635
158 E1K 0.8632
159 PZ8 0.8627
160 N1E 0.8627
161 SKF 0.8625
162 12T 0.8624
163 BGU 0.8622
164 4BF 0.8619
165 6P3 0.8618
166 CUH 0.8617
167 3VW 0.8617
168 PFF 0.8615
169 MFZ 0.8614
170 5NE 0.8614
171 G1P 0.8610
172 BP3 0.8609
173 HHS 0.8609
174 SG2 0.8607
175 EQW 0.8600
176 EAE 0.8599
177 A5P 0.8598
178 N2Z 0.8594
179 3XH 0.8593
180 J27 0.8592
181 P9E 0.8591
182 GFE 0.8590
183 B2Y 0.8587
184 IQ5 0.8579
185 HNK 0.8576
186 80G 0.8574
187 3D1 0.8573
188 S60 0.8573
189 3L1 0.8571
190 EF2 0.8571
191 RH1 0.8569
192 FWD 0.8567
193 8MO 0.8564
194 JOB 0.8558
195 3VX 0.8555
196 6FZ 0.8554
197 PH3 0.8550
198 4NP 0.8541
199 5SB 0.8540
200 G6P 0.8537
201 6HX 0.8534
202 FER 0.8533
203 CUT 0.8526
204 N91 0.8517
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 6SI3; Ligand: LEB; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 1) in the query (biounit: 6si3.bio2) has 21 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 2; Query (leader) PDB : 6SI3; Ligand: LEB; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 2) in the query (biounit: 6si3.bio1) has 24 residues
No: Leader PDB Ligand Sequence Similarity
APoc FAQ
Feedback