Receptor
PDB id Resolution Class Description Source Keywords
4AGQ 1.42 Å NON-ENZYME: BINDING STRUCTURE OF THE P53 CORE DOMAIN MUTANT Y220C BOUND TO THE STABILIZING SMALL MOLECULE PHIKAN5196 HOMO SAPIENS TRANSCRIPTION CELL CYCLE APOPTOSIS CANCER MUTATION SURFACREVICE PROTEIN FOLDING AGGREGATION MUTANT RESCUE SMALL-MOLECULE DRUG PROTEIN STABILIZATION HALOGEN BONDING
Ref.: HALOGEN-ENRICHED FRAGMENT LIBRARIES AS LEADS FOR DR RESCUE OF MUTANT P53. J.AM.CHEM.SOC. V. 134 6810 2012
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
P96 A:1291;
B:1290;
Valid;
Valid;
none;
none;
Kd = 9.7 uM
517.446 C25 H32 I N3 O CCN(C...
ZN A:1300;
B:1300;
Part of Protein;
Part of Protein;
none;
none;
submit data
65.409 Zn [Zn+2...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
4AGQ 1.42 Å NON-ENZYME: BINDING STRUCTURE OF THE P53 CORE DOMAIN MUTANT Y220C BOUND TO THE STABILIZING SMALL MOLECULE PHIKAN5196 HOMO SAPIENS TRANSCRIPTION CELL CYCLE APOPTOSIS CANCER MUTATION SURFACREVICE PROTEIN FOLDING AGGREGATION MUTANT RESCUE SMALL-MOLECULE DRUG PROTEIN STABILIZATION HALOGEN BONDING
Ref.: HALOGEN-ENRICHED FRAGMENT LIBRARIES AS LEADS FOR DR RESCUE OF MUTANT P53. J.AM.CHEM.SOC. V. 134 6810 2012
Members (22)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 473 families.
1 2X0W - X0W C10 H11 N O2 S Cc1nc2cc(c....
2 4AGM Kd = 104 uM P86 C16 H24 I2 N2 O CCN(CC)C1C....
3 5AB9 Kd = 470 uM 92O C15 H20 N2 CCc1cccc2c....
4 2X0V - X0V C7 H7 F3 N2 c1cc(c(cc1....
5 5G4O Kd = 28 uM O80 C17 H17 F3 N2 CN(C)Cc1cc....
6 5AOJ Kd = 21 uM Y0V C11 H7 I2 N O3 c1ccn(c1)c....
7 5AOL Kd = 4800 uM UFV C7 H6 Br F3 N2 c1c(cc(c(c....
8 5AOI Kd = 940 uM RZH C13 H17 Br N2 CCc1cc(cc2....
9 4AGP Kd = 20.6 uM P51 C25 H31 I N2 O2 CCN(CC)C1C....
10 3ZME - QC5 C17 H19 F N4 CN(C)CCn1c....
11 5AOK - GOH C11 H10 N6 O c1ccn(c1)c....
12 5A7B Kd = 271 uM KMN C27 H32 N2 O2 CCN(CC)C1C....
13 5ABA Kd = 1040 uM UL7 C17 H24 Br Cl N2 O2 c1c(cc(c(c....
14 2VUK Kd = 150 uM P83 C16 H18 N2 CCn1c2cccc....
15 4AGQ Kd = 9.7 uM P96 C25 H32 I N3 O CCN(CC)C1C....
16 4AGN Kd = 107 uM NXG C19 H27 I N2 O2 CCN(CC)C1C....
17 5AOM Kd = 1270 uM FY8 C12 H15 Cl N2 O2 c1cc(c(cc1....
18 2X0U - X0U C9 H8 N2 O2 S c1c2c(cc3c....
19 4AGO Kd = 15.5 uM P74 C24 H36 I N3 O3 CCN(CC)C1C....
20 5G4N Kd = 101 uM O83 C16 H16 F2 N2 CNCc1ccc2c....
21 4AGL Kd = 184 uM P84 C14 H20 I2 N2 O CN1CCC(CC1....
22 5G4M Kd = 138 uM O82 C16 H17 F N2 CNCc1ccc2c....
70% Homology Family (22)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 355 families.
1 2X0W - X0W C10 H11 N O2 S Cc1nc2cc(c....
2 4AGM Kd = 104 uM P86 C16 H24 I2 N2 O CCN(CC)C1C....
3 5AB9 Kd = 470 uM 92O C15 H20 N2 CCc1cccc2c....
4 2X0V - X0V C7 H7 F3 N2 c1cc(c(cc1....
5 5G4O Kd = 28 uM O80 C17 H17 F3 N2 CN(C)Cc1cc....
6 5AOJ Kd = 21 uM Y0V C11 H7 I2 N O3 c1ccn(c1)c....
7 5AOL Kd = 4800 uM UFV C7 H6 Br F3 N2 c1c(cc(c(c....
8 5AOI Kd = 940 uM RZH C13 H17 Br N2 CCc1cc(cc2....
9 4AGP Kd = 20.6 uM P51 C25 H31 I N2 O2 CCN(CC)C1C....
10 3ZME - QC5 C17 H19 F N4 CN(C)CCn1c....
11 5AOK - GOH C11 H10 N6 O c1ccn(c1)c....
12 5A7B Kd = 271 uM KMN C27 H32 N2 O2 CCN(CC)C1C....
13 5ABA Kd = 1040 uM UL7 C17 H24 Br Cl N2 O2 c1c(cc(c(c....
14 2VUK Kd = 150 uM P83 C16 H18 N2 CCn1c2cccc....
15 4AGQ Kd = 9.7 uM P96 C25 H32 I N3 O CCN(CC)C1C....
16 4AGN Kd = 107 uM NXG C19 H27 I N2 O2 CCN(CC)C1C....
17 5AOM Kd = 1270 uM FY8 C12 H15 Cl N2 O2 c1cc(c(cc1....
18 2X0U - X0U C9 H8 N2 O2 S c1c2c(cc3c....
19 4AGO Kd = 15.5 uM P74 C24 H36 I N3 O3 CCN(CC)C1C....
20 5G4N Kd = 101 uM O83 C16 H16 F2 N2 CNCc1ccc2c....
21 4AGL Kd = 184 uM P84 C14 H20 I2 N2 O CN1CCC(CC1....
22 5G4M Kd = 138 uM O82 C16 H17 F N2 CNCc1ccc2c....
50% Homology Family (22)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 272 families.
1 2X0W - X0W C10 H11 N O2 S Cc1nc2cc(c....
2 4AGM Kd = 104 uM P86 C16 H24 I2 N2 O CCN(CC)C1C....
3 5AB9 Kd = 470 uM 92O C15 H20 N2 CCc1cccc2c....
4 2X0V - X0V C7 H7 F3 N2 c1cc(c(cc1....
5 5G4O Kd = 28 uM O80 C17 H17 F3 N2 CN(C)Cc1cc....
6 5AOJ Kd = 21 uM Y0V C11 H7 I2 N O3 c1ccn(c1)c....
7 5AOL Kd = 4800 uM UFV C7 H6 Br F3 N2 c1c(cc(c(c....
8 5AOI Kd = 940 uM RZH C13 H17 Br N2 CCc1cc(cc2....
9 4AGP Kd = 20.6 uM P51 C25 H31 I N2 O2 CCN(CC)C1C....
10 3ZME - QC5 C17 H19 F N4 CN(C)CCn1c....
11 5AOK - GOH C11 H10 N6 O c1ccn(c1)c....
12 5A7B Kd = 271 uM KMN C27 H32 N2 O2 CCN(CC)C1C....
13 5ABA Kd = 1040 uM UL7 C17 H24 Br Cl N2 O2 c1c(cc(c(c....
14 2VUK Kd = 150 uM P83 C16 H18 N2 CCn1c2cccc....
15 4AGQ Kd = 9.7 uM P96 C25 H32 I N3 O CCN(CC)C1C....
16 4AGN Kd = 107 uM NXG C19 H27 I N2 O2 CCN(CC)C1C....
17 5AOM Kd = 1270 uM FY8 C12 H15 Cl N2 O2 c1cc(c(cc1....
18 2X0U - X0U C9 H8 N2 O2 S c1c2c(cc3c....
19 4AGO Kd = 15.5 uM P74 C24 H36 I N3 O3 CCN(CC)C1C....
20 5G4N Kd = 101 uM O83 C16 H16 F2 N2 CNCc1ccc2c....
21 4AGL Kd = 184 uM P84 C14 H20 I2 N2 O CN1CCC(CC1....
22 5G4M Kd = 138 uM O82 C16 H17 F N2 CNCc1ccc2c....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: P96; Similar ligands found: 6
No: Ligand ECFP6 Tc MDL keys Tc
1 P96 1 1
2 NXG 0.679487 0.915254
3 P51 0.666667 0.883333
4 P74 0.622222 0.797101
5 P86 0.493827 0.877193
6 KMN 0.47 0.816667
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 4AGQ; Ligand: P96; Similar sites found: 37
This union binding pocket(no: 1) in the query (biounit: 4agq.bio2) has 21 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 3QXV MTX 0.0009794 0.43232 None
2 4YEF 4CQ 0.01176 0.40678 None
3 1QGQ UDP 0.007182 0.42337 1.36986
4 2CFI ZZZ 0.01423 0.40861 1.36986
5 1YQC GLV 0.02734 0.40064 1.76471
6 4TTS 6DD 0.009006 0.40071 1.88679
7 2VDF OCT 0.006428 0.42631 2.28311
8 5EOB 5QQ 0.01133 0.42565 2.28311
9 4PVD NDP 0.008846 0.40714 2.73973
10 5HCY 60D 0.02344 0.40315 2.73973
11 5N9X THR 0.02886 0.40153 2.73973
12 1QXA GLY GLY GLY 0.0006343 0.49353 3.65297
13 5W4W 9WG 0.003659 0.42852 3.65297
14 2PT9 2MH 0.0109 0.41177 3.65297
15 2BVE PH5 0.01281 0.42054 4.20168
16 5KAX RHQ 0.02119 0.40423 4.21687
17 1QKQ MAN 0.002561 0.4236 4.22535
18 2CXG GLC GLC 0.01588 0.41276 4.56621
19 1U7Z PMT 0.0102 0.41198 4.56621
20 3QDK QDK 0.01874 0.41473 5.02283
21 4CQE CQE 0.01259 0.41104 5.47945
22 5F7J ADE 0.01839 0.41007 5.625
23 2G30 ALA ALA PHE 0.01536 0.40984 5.93607
24 3TW1 AHN 0.01939 0.40805 5.93607
25 2CJU PHX 0.02032 0.41044 6.61157
26 1VJY 460 0.007912 0.41462 8.21918
27 3ZJX BOG 0.01711 0.40869 8.21918
28 4TWP AXI 0.01654 0.41123 9.58904
29 3AB4 LYS 0.01355 0.40153 9.58904
30 5DEY 59T 0.01897 0.40171 10.5023
31 1OUK 084 0.0278 0.42754 12.7854
32 1UPR 4IP 0.01926 0.40257 13.0081
33 3KRR DQX 0.02702 0.4127 13.6986
34 4YFY 1YJ 0.007412 0.40251 15.5251
35 1U4L H1S 0.02776 0.40411 16.1765
36 2BOS GLA GAL GLC NBU 0.02227 0.41026 19.1176
37 2BOS GLA GAL GLC 0.02533 0.40603 19.1176
Pocket No.: 2; Query (leader) PDB : 4AGQ; Ligand: P96; Similar sites found: 31
This union binding pocket(no: 2) in the query (biounit: 4agq.bio1) has 24 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 2W5P CL8 0.0303 0.40315 1.34228
2 5JBE MAL 0.003942 0.45514 2.73973
3 4CLI 5P8 0.01556 0.40306 2.73973
4 4CC6 L5Y 0.02565 0.40077 2.73973
5 4YRD 3IT 0.009896 0.42592 3.19635
6 2JLD AG1 0.009705 0.40152 3.19635
7 4LH7 1X8 0.01195 0.43161 3.65297
8 1GPM AMP 0.01557 0.41804 3.65297
9 2WBV SIA 0.01272 0.44149 3.7037
10 3A6T 8OG 0.01196 0.40192 3.87597
11 3SJK LYS PRO VAL LEU ARG THR ALA 0.01247 0.42202 4.10959
12 5HVJ ANP 0.022 0.41164 5.02283
13 2OQ5 BEN 0.02377 0.40887 5.02283
14 4AZT LY2 0.02161 0.40061 5.02283
15 1JJ7 ADP 0.01253 0.42886 5.47945
16 4ZVI 4S4 0.005899 0.40876 5.47945
17 5TT6 ATP 0.005427 0.40373 6.09137
18 4CQK PIO 0.02329 0.40924 6.38298
19 5D9G GLU ASN LEU TYR PHE GLN 0.02027 0.40596 6.39269
20 4WNP 3RJ 0.01301 0.40024 6.39269
21 1CKM GTP 0.004694 0.43801 7.30594
22 5BVE 4VG 0.02328 0.40654 7.30594
23 3FW3 GLC 0.03001 0.40353 7.30594
24 4GGL CJC 0.004475 0.42549 8.37209
25 2XMY CDK 0.009209 0.42726 9.58904
26 1AV5 AP2 0.002647 0.44065 10.3175
27 4CS9 AMP 0.02259 0.40691 11.1111
28 3VSV XYS 0.002053 0.47154 16.895
29 4XBA 5GP 0.0002626 0.483 19
30 4XBA GMP 0.0004311 0.47833 19
31 2J73 GLC GLC GLC 0.006289 0.44854 20.3883
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