Receptor
PDB id Resolution Class Description Source Keywords
5AOJ 1.47 Å NON-ENZYME: BINDING STRUCTURE OF THE P53 CANCER MUTANT Y220C IN COMPLEX WITH 2-H 5-DIIODO-4-(1H-PYRROL-1-YL)BENZOIC ACID HOMO SAPIENS CELL CYCLE P53 CANCER TUMOR SUPPRESSION DNA BINDING CANTHERAPY SMALL-MOLECULE STABILIZERS MOLECULAR CHAPERONE
Ref.: EXPLOITING TRANSIENT PROTEIN STATES FOR THE DESIGN SMALL-MOLECULE STABILIZERS OF MUTANT P53. STRUCTURE V. 23 2246 2015
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
ZN A:1300;
B:1300;
 Part of Protein;
Part of Protein;
 none;
none;
 submit data
65.409 Zn [Zn+2...
Y0V B:1292;
A:1291;
 Valid;
Valid;
 none;
none;
 Kd = 21 uM
454.987 C11 H7 I2 N O3 c1ccn...
PEG B:1291;
 Invalid;
 none;
 submit data
106.12 C4 H10 O3 C(COC...
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: Y0V; Similar ligands found: 9
No: Ligand ECFP6 Tc MDL keys Tc
1 Y0V 1 1
2 9H5 0.52459 0.6
3 9GN 0.491803 0.811321
4 9GW 0.491803 0.811321
5 9GT 0.483871 0.86
6 9GZ 0.483871 0.955556
7 9GQ 0.47619 0.781818
8 9H2 0.461538 0.833333
9 9GK 0.434783 0.843137
Similar Ligands (3D)
Ligand no: 1; Ligand: Y0V; Similar ligands found: 208
No: Ligand Similarity coefficient
1 NDG 0.9522
2 NAG 0.9480
3 GDL 0.9409
4 AU8 0.9398
5 LOG 0.9370
6 SNG 0.9297
7 EV2 0.9268
8 MAG 0.9263
9 BNX 0.9258
10 0OK 0.9258
11 9KZ 0.9213
12 0FR 0.9187
13 L1O 0.9175
14 MQG 0.9175
15 NGA 0.9150
16 BGN 0.9129
17 B52 0.9127
18 3R4 0.9126
19 ST2 0.9126
20 XCG 0.9100
21 FYR 0.9099
22 3UG 0.9094
23 3XR 0.9090
24 KF5 0.9085
25 OA4 0.9080
26 0J4 0.9077
27 89J 0.9059
28 S0G 0.9054
29 OQC 0.9053
30 7EH 0.9051
31 68A 0.9048
32 VC3 0.9048
33 1A5 0.9046
34 A2G 0.9036
35 54E 0.9029
36 PQS 0.9023
37 KMY 0.9021
38 LP8 0.9021
39 9FH 0.9018
40 22T 0.9007
41 CP7 0.9000
42 363 0.8997
43 JO5 0.8995
44 4CN 0.8993
45 27B 0.8993
46 4AB 0.8978
47 92O 0.8976
48 HBI 0.8972
49 H2B 0.8972
50 RVE 0.8970
51 2P3 0.8970
52 NYJ 0.8968
53 2JX 0.8967
54 H4B 0.8964
55 H75 0.8961
56 BA5 0.8944
57 ZSP 0.8942
58 S7D 0.8938
59 BIO 0.8937
60 S0D 0.8936
61 RKN 0.8934
62 CC5 0.8930
63 KP2 0.8928
64 A4N 0.8919
65 6P3 0.8910
66 FCW 0.8910
67 3QI 0.8906
68 1BW 0.8902
69 GJP 0.8885
70 FF2 0.8880
71 NPS 0.8872
72 QME 0.8866
73 EAE 0.8865
74 HNT 0.8856
75 657 0.8855
76 NPX 0.8854
77 6E8 0.8849
78 G14 0.8847
79 E6Q 0.8841
80 EF2 0.8829
81 A5Q 0.8821
82 CHQ 0.8820
83 CP6 0.8812
84 BHS 0.8811
85 BHQ 0.8808
86 AWE 0.8806
87 3AK 0.8804
88 JOB 0.8800
89 PZ8 0.8796
90 ST1 0.8795
91 A4T 0.8793
92 A9K 0.8792
93 MNS 0.8791
94 2F8 0.8779
95 BBK 0.8779
96 F4K 0.8776
97 JXK 0.8776
98 7L4 0.8772
99 TC8 0.8766
100 PTB 0.8764
101 RSV 0.8762
102 PMP 0.8761
103 SJK 0.8759
104 PLP 0.8758
105 N1E 0.8758
106 3XH 0.8756
107 3DE 0.8750
108 5AD 0.8746
109 42R 0.8739
110 3N1 0.8738
111 3VX 0.8737
112 RH1 0.8734
113 549 0.8734
114 12T 0.8733
115 TRP 0.8726
116 1CY 0.8726
117 0GA 0.8726
118 0OO 0.8724
119 0J5 0.8721
120 DHC 0.8721
121 ZEC 0.8718
122 M3F 0.8717
123 N2M 0.8716
124 AUT 0.8714
125 2J1 0.8711
126 IQ5 0.8710
127 21D 0.8709
128 6EL 0.8708
129 S0E 0.8705
130 G6P 0.8703
131 PH2 0.8701
132 4NP 0.8701
133 3D1 0.8697
134 Y70 0.8695
135 1QV 0.8695
136 MFZ 0.8683
137 QBP 0.8681
138 3L1 0.8680
139 YZ9 0.8679
140 4FC 0.8677
141 X04 0.8676
142 SKF 0.8675
143 3VS 0.8674
144 CUH 0.8670
145 NDD 0.8670
146 SNO 0.8668
147 GF4 0.8664
148 KLV 0.8662
149 LZB 0.8662
150 GEN 0.8661
151 FY8 0.8661
152 X0T 0.8659
153 K82 0.8656
154 7N8 0.8655
155 HHS 0.8654
156 B56 0.8652
157 K4V 0.8651
158 DAH 0.8649
159 N91 0.8645
160 I2E 0.8644
161 9R5 0.8640
162 5F1 0.8639
163 6J5 0.8638
164 F5C 0.8638
165 4MB 0.8637
166 C1M 0.8637
167 F4U 0.8636
168 39Z 0.8634
169 QIV 0.8633
170 CTE 0.8633
171 EUE 0.8630
172 CPZ 0.8630
173 4AF 0.8629
174 BGU 0.8628
175 72D 0.8628
176 LVY 0.8626
177 0ON 0.8618
178 5B2 0.8618
179 L3L 0.8618
180 4NS 0.8614
181 PNP 0.8614
182 KMP 0.8611
183 S60 0.8610
184 S8A 0.8601
185 PQM 0.8601
186 A4Q 0.8596
187 X0U 0.8593
188 SG2 0.8586
189 6HP 0.8585
190 FMQ 0.8584
191 80G 0.8583
192 GC2 0.8583
193 8MO 0.8579
194 MD6 0.8575
195 5GT 0.8571
196 TGW 0.8570
197 I4D 0.8566
198 GO2 0.8564
199 E1K 0.8564
200 DC5 0.8561
201 J6W 0.8560
202 RNO 0.8559
203 W81 0.8559
204 3WJ 0.8554
205 IOS 0.8539
206 DBS 0.8534
207 LZJ 0.8522
208 3AE 0.8505
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
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