Receptor
PDB id Resolution Class Description Source Keywords
2GV2 1.8 Å EC: 6.3.2.- MDM2 IN COMPLEX WITH AN 8-MER P53 PEPTIDE ANALOGUE HOMO SAPIENS OPTIMIZED PROTEIN-PROTEIN INTERACTION. SYNTHETIC PEPTIDE. ALPHA HELIX BINDING PROTEIN LIGASE
Ref.: CRYSTALLOGRAPHIC ANALYSIS OF AN 8-MER P53 PEPTIDE ANALOGUE COMPLEXED WITH MDM2. J.AM.CHEM.SOC. V. 128 11000 2006
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
ACE PHE MET AIB PM3 6CW GLU 1AC LEU B:1;
Valid;
none;
ic50 = 5 nM
1207.72 n/a Clc1c...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
4WT2 1.42 Å EC: 6.3.2.- CO-CRYSTAL STRUCTURE OF MDM2 IN COMPLEX WITH AM-7209 HOMO SAPIENS P53 PROTEIN-PROTEIN INTERACTION LIGASE-LIGASE INHIBITOR CO
Ref.: DISCOVERY OF AM-7209, A POTENT AND SELECTIVE 4-AMID ACID INHIBITOR OF THE MDM2-P53 INTERACTION. J.MED.CHEM. V. 57 10499 2014
Members (5)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 34 families.
1 2GV2 ic50 = 5 nM ACE PHE MET AIB PM3 6CW GLU 1AC LEU n/a n/a
2 5HMK ic50 = 0.04 uM 62Q C35 H38 F6 N4 O5 CCC[C@@H]1....
3 5TRF Ki = 0.88 nM 7HC C29 H34 Cl2 F N3 O3 CC(C)(C)C[....
4 4WT2 Kd = 39 pM 3UD C37 H41 Cl2 F N2 O7 S C[C@@]1(C[....
5 4OGT ic50 = 0.1 nM 2U6 C33 H36 Cl2 N2 O6 S C[C@]1(C(=....
70% Homology Family (54)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 23 families.
1 3JZK ic50 = 1.23 uM YIN C24 H16 Br2 N4 O c1ccc2c(c1....
2 4JV7 ic50 = 1 uM 1MN C24 H21 Br2 N O2 CN1[C@@H](....
3 4JVR ic50 = 9.4 nM 1MT C25 H29 Cl2 F N4 O2 CC(C)(C)C[....
4 5LN2 ic50 = 0.13 nM 6ZT C32 H34 Cl2 N4 O3 Cc1cc(ccc1....
5 4ZFI Kd = 0.5 uM 4NJ C27 H21 Cl3 N2 O2 CN1C(=O)C(....
6 4ZYF Ki = 1.3 nM 4T4 C38 H47 Cl N4 O4 CC(C)Oc1cc....
7 4DIJ ic50 = 0.03 uM BLF C31 H29 Cl2 N5 O2 c1ccc(cc1)....
8 4ZYI ic50 = 0.008 uM 4TH C33 H34 Cl N3 O3 CC[C@@H](C....
9 5HMH ic50 = 0.007 uM 62R C35 H38 F6 N4 O6 S CCC[C@@H]1....
10 4OAS Kd = 0.045 nM 2SW C28 H35 Cl2 N O5 S CC[C@@H](C....
11 4ERF ic50 = 1.1 nM 0R3 C25 H29 Cl2 N O4 CC[C@@H]([....
12 4ZYC ic50 = 0.38 uM 4SS C28 H28 Cl N5 O4 CCOc1cc2c(....
13 4OCC ic50 = 2 nM 2TZ C26 H31 Cl2 N O6 S CC[C@@H](C....
14 3LBL Ki = 36 nM MI6 C29 H35 Cl2 F N4 O3 CC(C)(C)C[....
15 4MDN Ki = 0.6 uM Y30 C30 H29 Cl2 N3 O5 CC(C)(C)NC....
16 5HMI ic50 = 0.015 uM 62T C33 H36 F6 N4 O5 S CCC[C@@H]1....
17 4MDQ Ki = 1.2 uM 28W C24 H28 Cl N5 O5 CC(C)C[C@@....
18 4HG7 ic50 = 90 nM NUT C30 H30 Cl2 N4 O4 CC(C)Oc1cc....
19 3W69 ic50 = 8.3 nM LTZ C36 H43 Cl2 N5 O3 S CC[C@@H]1C....
20 4OQ3 ic50 = 0.008 uM 2V8 C24 H18 Cl2 N2 O2 Cc1cccc(c1....
21 4JV9 ic50 = 1.8 uM 1MO C24 H21 Cl2 N O2 CN1[C@@H](....
22 4QOC ic50 = 0.12 nM 35T C29 H34 Cl2 N2 O5 S C[C@@]1(C[....
23 4OGV ic50 = 9 nM 2U7 C26 H31 Cl2 N O6 S CC[C@@H](C....
24 4ZGK Kd = 3.1 uM 4NX C26 H18 Cl3 N O3 c1cc(ccc1C....
25 4OBA ic50 = 0.4 nM 2TW C27 H31 Cl2 N O6 S CC(C)(C)S(....
26 4JVE ic50 = 0.086 uM 1MQ C28 H24 Cl2 F N O4 C/C=C/[C@H....
27 4JWR ic50 = 0.61 uM 1MY C22 H23 Cl2 N O5 CC[C@@H](C....
28 4ERE ic50 = 4.2 nM 0R2 C27 H31 Cl2 N O5 CC[C@@H](C....
29 4QO4 ic50 = 0.005 uM 35S C31 H32 Cl2 N2 O3 CC[C@@H](c....
30 4LWU ic50 = 0.005 uM 20U C30 H29 Cl2 F N4 O3 CC(C)(C)C[....
31 4LWV ic50 = 7 nM 20W C29 H29 Cl2 F N4 O4 S CC(C)(C)C[....
32 4J74 Kd = 26 uM I18 C16 H14 Cl2 N2 CC1=N[C@H]....
33 4IPF ic50 = 18 nM 1F0 C38 H48 Cl2 N4 O4 S CCOc1cc(cc....
34 4J7D Kd = 20 uM I31 C29 H32 Cl2 N2 O CCOc1cc(cc....
35 4J3E ic50 = 0.088 uM NUT C30 H30 Cl2 N4 O4 CC(C)Oc1cc....
36 4JSC ic50 = 56 nM 1OY C27 H31 Cl2 F2 N3 O3 CC(C)(C)C[....
37 4JRG ic50 = 196 nM I09 C27 H33 Cl2 N3 O3 CC(C)(C)C[....
38 4J7E Kd = 14 uM I29 C27 H34 Cl2 N4 O3 S CC1=N[C@@]....
39 4LWT ic50 = 3.9 uM 20Q C22 H22 Cl2 N2 O2 CC(=O)N1CC....
40 5J7F - 6GG C35 H33 Cl2 F N4 O5 c1cc(ccc1C....
41 4HBM Kd = 8.2 nM 0Y7 C23 H25 Cl2 N O4 CC[C@@H](C....
42 3TU1 Ki = 0.25 uM 07G C23 H21 Cl F2 N3 O4 CC(C)(C)NC....
43 2AXI ic50 = 140 nM PRO PHE GLU 6CW LEU ASP TRP GLU PHE DPR n/a n/a
44 5J7G - 6GG C35 H33 Cl2 F N4 O5 c1cc(ccc1C....
45 1T4F - ARG PHE MET ASP TYR TRP GLU GLY LEU n/a n/a
46 2GV2 ic50 = 5 nM ACE PHE MET AIB PM3 6CW GLU 1AC LEU n/a n/a
47 5HMK ic50 = 0.04 uM 62Q C35 H38 F6 N4 O5 CCC[C@@H]1....
48 5TRF Ki = 0.88 nM 7HC C29 H34 Cl2 F N3 O3 CC(C)(C)C[....
49 4WT2 Kd = 39 pM 3UD C37 H41 Cl2 F N2 O7 S C[C@@]1(C[....
50 4OGT ic50 = 0.1 nM 2U6 C33 H36 Cl2 N2 O6 S C[C@]1(C(=....
51 1RV1 ic50 = 0.14 uM IMZ C31 H34 Br2 N4 O4 CCOc1cc(cc....
52 4ODF ic50 = 0.1 nM 2U1 C33 H36 Cl2 N2 O6 S C[C@@]1(C(....
53 4ODE ic50 = 0.1 nM 2U0 C33 H37 Cl2 F N2 O5 S2 C[C@@]1(C[....
54 4OGN ic50 = 0.1 nM 2U5 C34 H38 Cl2 N2 O5 S C[C@@]1(C[....
50% Homology Family (57)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 18 families.
1 3JZK ic50 = 1.23 uM YIN C24 H16 Br2 N4 O c1ccc2c(c1....
2 4JV7 ic50 = 1 uM 1MN C24 H21 Br2 N O2 CN1[C@@H](....
3 4JVR ic50 = 9.4 nM 1MT C25 H29 Cl2 F N4 O2 CC(C)(C)C[....
4 5LN2 ic50 = 0.13 nM 6ZT C32 H34 Cl2 N4 O3 Cc1cc(ccc1....
5 4ZFI Kd = 0.5 uM 4NJ C27 H21 Cl3 N2 O2 CN1C(=O)C(....
6 4ZYF Ki = 1.3 nM 4T4 C38 H47 Cl N4 O4 CC(C)Oc1cc....
7 4DIJ ic50 = 0.03 uM BLF C31 H29 Cl2 N5 O2 c1ccc(cc1)....
8 4ZYI ic50 = 0.008 uM 4TH C33 H34 Cl N3 O3 CC[C@@H](C....
9 5HMH ic50 = 0.007 uM 62R C35 H38 F6 N4 O6 S CCC[C@@H]1....
10 4OAS Kd = 0.045 nM 2SW C28 H35 Cl2 N O5 S CC[C@@H](C....
11 4ERF ic50 = 1.1 nM 0R3 C25 H29 Cl2 N O4 CC[C@@H]([....
12 4ZYC ic50 = 0.38 uM 4SS C28 H28 Cl N5 O4 CCOc1cc2c(....
13 4OCC ic50 = 2 nM 2TZ C26 H31 Cl2 N O6 S CC[C@@H](C....
14 3LBL Ki = 36 nM MI6 C29 H35 Cl2 F N4 O3 CC(C)(C)C[....
15 4MDN Ki = 0.6 uM Y30 C30 H29 Cl2 N3 O5 CC(C)(C)NC....
16 5HMI ic50 = 0.015 uM 62T C33 H36 F6 N4 O5 S CCC[C@@H]1....
17 4MDQ Ki = 1.2 uM 28W C24 H28 Cl N5 O5 CC(C)C[C@@....
18 4HG7 ic50 = 90 nM NUT C30 H30 Cl2 N4 O4 CC(C)Oc1cc....
19 3W69 ic50 = 8.3 nM LTZ C36 H43 Cl2 N5 O3 S CC[C@@H]1C....
20 4OQ3 ic50 = 0.008 uM 2V8 C24 H18 Cl2 N2 O2 Cc1cccc(c1....
21 4JV9 ic50 = 1.8 uM 1MO C24 H21 Cl2 N O2 CN1[C@@H](....
22 4QOC ic50 = 0.12 nM 35T C29 H34 Cl2 N2 O5 S C[C@@]1(C[....
23 4OGV ic50 = 9 nM 2U7 C26 H31 Cl2 N O6 S CC[C@@H](C....
24 4ZGK Kd = 3.1 uM 4NX C26 H18 Cl3 N O3 c1cc(ccc1C....
25 4OBA ic50 = 0.4 nM 2TW C27 H31 Cl2 N O6 S CC(C)(C)S(....
26 4JVE ic50 = 0.086 uM 1MQ C28 H24 Cl2 F N O4 C/C=C/[C@H....
27 4JWR ic50 = 0.61 uM 1MY C22 H23 Cl2 N O5 CC[C@@H](C....
28 4ERE ic50 = 4.2 nM 0R2 C27 H31 Cl2 N O5 CC[C@@H](C....
29 4QO4 ic50 = 0.005 uM 35S C31 H32 Cl2 N2 O3 CC[C@@H](c....
30 4LWU ic50 = 0.005 uM 20U C30 H29 Cl2 F N4 O3 CC(C)(C)C[....
31 4LWV ic50 = 7 nM 20W C29 H29 Cl2 F N4 O4 S CC(C)(C)C[....
32 4J74 Kd = 26 uM I18 C16 H14 Cl2 N2 CC1=N[C@H]....
33 4IPF ic50 = 18 nM 1F0 C38 H48 Cl2 N4 O4 S CCOc1cc(cc....
34 4J7D Kd = 20 uM I31 C29 H32 Cl2 N2 O CCOc1cc(cc....
35 4J3E ic50 = 0.088 uM NUT C30 H30 Cl2 N4 O4 CC(C)Oc1cc....
36 4JSC ic50 = 56 nM 1OY C27 H31 Cl2 F2 N3 O3 CC(C)(C)C[....
37 4JRG ic50 = 196 nM I09 C27 H33 Cl2 N3 O3 CC(C)(C)C[....
38 4J7E Kd = 14 uM I29 C27 H34 Cl2 N4 O3 S CC1=N[C@@]....
39 4LWT ic50 = 3.9 uM 20Q C22 H22 Cl2 N2 O2 CC(=O)N1CC....
40 5J7F - 6GG C35 H33 Cl2 F N4 O5 c1cc(ccc1C....
41 4HBM Kd = 8.2 nM 0Y7 C23 H25 Cl2 N O4 CC[C@@H](C....
42 3TU1 Ki = 0.25 uM 07G C23 H21 Cl F2 N3 O4 CC(C)(C)NC....
43 2AXI ic50 = 140 nM PRO PHE GLU 6CW LEU ASP TRP GLU PHE DPR n/a n/a
44 5J7G - 6GG C35 H33 Cl2 F N4 O5 c1cc(ccc1C....
45 1T4F - ARG PHE MET ASP TYR TRP GLU GLY LEU n/a n/a
46 3U15 ic50 = 41 nM 03M C20 H14 Cl F2 N3 O2 Cc1c(ccc2c....
47 3FE7 Kd = 75 nM ACE PHE MET AIB PM3 TRP GLU 1AC LEU NH2 n/a n/a
48 3FEA Kd = 36 nM ACE PHE MET AIB PM3 6CW GLU 1AC LEU NH2 n/a n/a
49 2GV2 ic50 = 5 nM ACE PHE MET AIB PM3 6CW GLU 1AC LEU n/a n/a
50 5HMK ic50 = 0.04 uM 62Q C35 H38 F6 N4 O5 CCC[C@@H]1....
51 5TRF Ki = 0.88 nM 7HC C29 H34 Cl2 F N3 O3 CC(C)(C)C[....
52 4WT2 Kd = 39 pM 3UD C37 H41 Cl2 F N2 O7 S C[C@@]1(C[....
53 4OGT ic50 = 0.1 nM 2U6 C33 H36 Cl2 N2 O6 S C[C@]1(C(=....
54 1RV1 ic50 = 0.14 uM IMZ C31 H34 Br2 N4 O4 CCOc1cc(cc....
55 4ODF ic50 = 0.1 nM 2U1 C33 H36 Cl2 N2 O6 S C[C@@]1(C(....
56 4ODE ic50 = 0.1 nM 2U0 C33 H37 Cl2 F N2 O5 S2 C[C@@]1(C[....
57 4OGN ic50 = 0.1 nM 2U5 C34 H38 Cl2 N2 O5 S C[C@@]1(C[....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: ACE PHE MET AIB PM3 6CW GLU 1AC LEU; Similar ligands found: 6
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 4WT2; Ligand: 3UD; Similar sites found: 69
This union binding pocket(no: 1) in the query (biounit: 4wt2.bio1) has 74 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 3B6C SDN 0.001063 0.48488 None
2 4YV5 SVR 0.002923 0.45853 None
3 1SBR VIB 0.01051 0.43242 None
4 1TMX HGX 0.003203 0.42131 None
5 4UCC ZKW 0.01862 0.42102 None
6 3ZLR X0B 0.002126 0.42077 None
7 3KP6 SAL 0.03762 0.41643 None
8 5UC9 MYR 0.02459 0.4146 None
9 1ECM TSA 0.0216 0.41161 None
10 4QOS ADP 0.0154 0.40754 None
11 4V3I ASP LEU THR ARG PRO 0.04302 0.40498 None
12 1R55 097 0.03491 0.40077 None
13 2JFZ 003 0.006167 0.41973 2.85714
14 2JFZ DGL 0.007142 0.41701 2.85714
15 5AZC PGT 0.0155 0.4126 2.85714
16 1W2D ADP 0.02779 0.40211 2.85714
17 3BPX SAL 0.03957 0.4021 2.85714
18 2V57 PRL 0.04528 0.4018 3.80952
19 1M2Z BOG 0.0001723 0.56869 4.7619
20 3RY9 1CA 0.003799 0.4287 4.7619
21 2Q2Y MKR 0.01745 0.40876 4.7619
22 2Q2Y ADP 0.01745 0.40876 4.7619
23 4UBS DIF 0.009188 0.44531 5.71429
24 2I0G I0G 0.0051 0.41705 5.71429
25 2FDW D3G 0.0227 0.41049 5.71429
26 4ZOM 4Q3 0.01905 0.40546 5.71429
27 3AB4 THR 0.03017 0.40407 5.71429
28 3QCQ 3Q0 0.02756 0.40297 5.71429
29 2FN8 RIP 0.04014 0.40278 5.71429
30 4MNS 2AX 0.002756 0.42641 6.66667
31 4RW3 SHV 0.03891 0.41568 6.66667
32 2JHP GUN 0.02028 0.40754 6.66667
33 3KDU NKS 0.00137 0.43896 7.61905
34 1DKF BMS 0.001112 0.43742 7.61905
35 3SP6 IL2 0.002511 0.43307 7.61905
36 2NPA MMB 0.00234 0.42718 7.61905
37 5HCV 60R 0.003882 0.42107 7.61905
38 1K7L 544 0.001825 0.41869 7.61905
39 2Z7I 742 0.01043 0.41453 7.61905
40 5F2T PLM 0.01001 0.41289 7.61905
41 2BJ4 OHT 0.0005055 0.40513 7.61905
42 1PU7 39A 0.02332 0.40066 8.57143
43 4LY9 1YY 0.01103 0.40061 9.52381
44 5ICK FEZ 0.01051 0.40516 10.4762
45 3OKI OKI 0.01044 0.40215 10.4762
46 5L2J 70E 0.005812 0.42488 11.2245
47 5L2J 6UL 0.005807 0.42359 11.2245
48 5OCA 9QZ 0.002579 0.47476 11.4286
49 5LIA 6XN 0.008359 0.41807 12.381
50 5HTX ADP 0.01705 0.41285 12.381
51 4JOB TLA 0.02807 0.40812 12.381
52 1TV5 N8E 0.00003978 0.57955 13.3333
53 4ORM ORO 0.01258 0.40916 13.3333
54 4ORM FMN 0.01258 0.40916 13.3333
55 4ORM 2V6 0.01258 0.40916 13.3333
56 1T0S BML 0.03215 0.40056 14.2857
57 4MRP GSH 0.04833 0.41178 15.2381
58 5LX9 OLB 0.01808 0.40419 15.2381
59 5K53 STE 0.007851 0.40761 16.1905
60 1LNX URI 0.006825 0.44611 17.284
61 5AAV GW5 0.001778 0.43951 20.9524
62 2QZO KN1 0.002749 0.43131 20.9524
63 4MGA 27L 0.01395 0.42786 20.9524
64 3E85 BSU 0.003756 0.41307 20.9524
65 1Y75 NAG 0.0236 0.40961 21.9048
66 4OAR 2S0 0.0001572 0.4193 23.8095
67 1SR7 MOF 0.003187 0.40763 23.8095
68 5EW9 5VC 0.02321 0.41208 33.3333
69 3HUN ZZ7 0.04111 0.40321 44.7619
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