Receptor
PDB id Resolution Class Description Source Keywords
6GDM 1.91 Å EC: 2.7.11.24 FRAGMENT-BASED DISCOVERY OF A HIGHLY POTENT, ORALLY BIOAVAIL INHIBITOR WHICH MODULATES THE PHOSPHORYLATION AND CATALYTICO F ERK1/2 HOMO SAPIENS ERK2 KINASE INHIBITOR SIGNALING PROTEIN
Ref.: FRAGMENT-BASED DISCOVERY OF A POTENT, ORALLY BIOAVA INHIBITOR THAT MODULATES THE PHOSPHORYLATION AND CA ACTIVITY OF ERK1/2. J. MED. CHEM. V. 61 4978 2018
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
F3Z A:404;
 Valid;
 none;
 submit data
587.674 C33 H33 N9 O2 c1cnc...
SO4 A:403;
A:401;
 Invalid;
Invalid;
 none;
none;
 submit data
96.063 O4 S [O-]S...
DMS A:402;
 Invalid;
 none;
 submit data
78.133 C2 H6 O S CS(=O...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
5BVE 2 Å EC: 2.7.11.24 TETRAHYDROPYRROLO-DIAZEPENONES AS INHIBITORS OF ERK2 KINASE HOMO SAPIENS INHIBITOR KINASE TRANSFERASE-TRANSFERASE INHIBITOR COMPLEX
Ref.: TETRAHYDROPYRROLO-DIAZEPENONES AS INHIBITORS OF ERK BIOORG.MED.CHEM.LETT. V. 25 3788 2015
Members (87)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 16 families.
1 6GDM - F3Z C33 H33 N9 O2 c1cnc(nc1)....
2 4XP3 - DX4 C5 H5 N5 S c1[nH]c2c(....
3 6QAQ - HVQ C5 H8 N S c1cscc1C[N....
4 4O6E ic50 = 1 nM 2SH C21 H25 Cl F N5 O3 c1cc(c(cc1....
5 5NHJ ic50 < 0.0003 uM 8XE C18 H21 N7 O2 Cn1c(ccn1)....
6 4QYY Kd = 0.05 uM 3G7 C25 H29 Cl N4 O4 CC(=O)c1cc....
7 6QAG - HUH C2 H3 N3 c1cnn[nH]1
8 4I5H Ki < 2 nM G17 C26 H21 F3 N4 O Cc1ccc(cc1....
9 6G93 ic50 = 11 nM EU2 C17 H17 Cl N4 O2 c1cc2c(cc1....
10 4QTE Kd = 0.084 uM 390 C24 H20 Cl2 F N5 O2 Cc1cnc(nc1....
11 4XNE - TT4 C8 H9 N5 c1ccc(cc1)....
12 3QYW - 6PB C11 H8 Br N5 c1cc(cc(c1....
13 5BUE ic50 = 0.003 uM 4V8 C23 H21 N5 O c1ccc(cc1)....
14 6GE0 ic50 = 2.1 nM EVQ C28 H30 Cl N5 O4 C[C@H](c1c....
15 6G9N ic50 = 3 nM ESN C29 H32 Cl N5 O4 Cc1cccc(c1....
16 2Z7L - S91 C20 H19 N5 O3 Cc1cccc(c1....
17 6QAW - HVE C12 H18 N5 c1c[nH]c2c....
18 4ZXT - CAQ C6 H6 O2 c1ccc(c(c1....
19 1WZY ic50 = 0.56 uM F29 C21 H17 N7 C=CCn1c2c(....
20 6DMG - EK6 C27 H26 Cl2 F N5 O4 CCOC(=O)CN....
21 5NHH ic50 < 0.00113 uM 8XH C19 H25 N5 O3 COCCN1CCc2....
22 6OPH - 6QB C21 H18 Cl F N6 O2 Cn1c(ccn1)....
23 6G9H ic50 = 4 nM ERW C24 H30 Cl N5 O3 CC(C)(C)N(....
24 4N4S - 2H1 C25 H24 N6 O Cc1cc(cc2c....
25 4QP8 ic50 = 0.28 uM 362 C14 H10 N6 c1cc(cnc1)....
26 6SLG Kd = 0.00000145 M LHZ C24 H24 F2 N8 O2 Cc1cnc(nc1....
27 4QP4 - 36O C11 H15 N5 c1[nH]c2c(....
28 6G9D ic50 = 4.3 nM ER8 C23 H28 Cl N5 O3 CC(C)(C)NC....
29 6GJB ic50 = 0.008 uM F0H C35 H34 Cl F N6 O4 c1cc(c(cc1....
30 6G91 ic50 = 3200 nM EQW C9 H12 Cl N3 O c1c(cnc(n1....
31 6G8X - EQT C7 H6 Cl N3 c1cc2c(c(c....
32 6DCG ic50 = 7 nM G67 C37 H41 N9 O3 S CC(C)Oc1cc....
33 4QP9 ic50 = 0.071 uM 35X C17 H16 N6 CCCn1cc(cn....
34 5BVE ic50 = 0.01 nM 4VG C25 H28 Cl N5 O3 c1cc(cc(c1....
35 6Q7S - IPH C6 H6 O c1ccc(cc1)....
36 5KE0 - 6S9 C20 H18 N6 O Cc1cc(ccn1....
37 6CPW ic50 = 5.6 nM F8V C35 H35 F N8 O2 S CS[C@]1(CC....
38 4XOY - DX4 C5 H5 N5 S c1[nH]c2c(....
39 6G9K - ESK C27 H28 Cl N5 O4 c1ccc(cc1)....
40 3QYZ - Z8B C10 H11 Br N8 O3 c1nc(c2c(n....
41 5BVF ic50 = 0.19 nM 4VJ C25 H28 Cl N5 O3 c1cc(cc(c1....
42 6G9M ic50 = 7.9 nM ESW C28 H30 Cl N5 O3 CC(C)(c1cc....
43 6QAH - HVB C3 H9 N2 CCC(=[NH2+....
44 6QA3 - PZO C3 H4 N2 c1c[nH]nc1
45 4XOZ - 620 C15 H16 N6 O c1ccc(cc1)....
46 5HD7 - 38Z C33 H33 N9 O2 c1cnc(nc1)....
47 4XRJ - 620 C15 H16 N6 O c1ccc(cc1)....
48 2OJJ Ki = 0.002 uM 82A C22 H17 Cl2 F N4 O2 c1cc(cc(c1....
49 6Q7K - 2AI C3 H5 N3 c1cnc([nH]....
50 4QTA Kd = 0.013 uM 38Z C33 H33 N9 O2 c1cnc(nc1)....
51 6RQ4 - KE8 C22 H27 N7 O2 S CC1(c2c(cc....
52 5NHO ic50 < 0.0003 uM 8XN C20 H25 N7 O2 Cc1cnc(nc1....
53 2OJG Ki = 2.3 uM 19A C16 H16 N4 O CN(C)C(=O)....
54 4XP0 - 42A C8 H5 N3 c1cc2c(c[n....
55 4QP2 Kd = 940 uM 36R C7 H5 Cl N2 O c1cc2c(cc1....
56 5NHF ic50 = 0.0012 uM 8X5 C23 H25 N5 O2 c1ccc(cc1)....
57 5BUJ ic50 = 0.005 uM 4VB C16 H15 N5 O c1cnccc1c2....
58 6G9J ic50 = 4.1 nM ERK C27 H28 Cl N5 O3 C[C@H](c1c....
59 5BUI ic50 = 0.089 uM 4V9 C17 H15 F N4 c1ccnc(c1)....
60 4QP7 ic50 = 5.9 uM 363 C9 H7 N5 c1c[nH]c2c....
61 3ERK ic50 = 18 uM SB4 C18 H19 F N6 c1cc(ccc1c....
62 6GDQ - EVK C21 H22 Cl2 N4 O2 CC(C)Nc1cc....
63 5V60 - ACP C11 H18 N5 O12 P3 c1nc(c2c(n....
64 6QA1 - HVK C5 H6 N2 c1ccnc(c1)....
65 1TVO Ki = 0.14 uM FRZ C18 H13 N7 c1ccc(cc1)....
66 6G9A ic50 = 21 nM ESQ C23 H28 Cl N5 O3 c1cc2c(cc1....
67 5BVD ic50 = 0.16 nM 4VF C24 H26 Cl N5 O3 c1cc(cc(c1....
68 4ZZN ic50 = 0.26 uM CQ8 C18 H21 Cl N4 O2 CNC(=O)c1c....
69 3SA0 - NRA C13 H8 O6 c1c(cc2c(c....
70 4ERK ic50 = 27 uM OLO C15 H18 N6 O Cn1cnc2c1n....
71 6GJD ic50 = 0.022 uM F0E C46 H55 N11 O5 c1cnc(nc1)....
72 5U6I - 81Y C19 H22 N4 O2 CC(C)Oc1cc....
73 5NHV ic50 = 0.0028 uM 8QB C16 H19 N5 O2 c1cnc(nc1c....
74 6QAL - HV2 C3 H6 O3 S C1C(CS1(=O....
75 3I5Z Ki = 2 nM Z48 C24 H23 N5 O2 Cc1cnc(nc1....
76 6QA4 - HRZ C5 H5 N O C1=CC(=O)N....
77 4N0S - DHC C9 H8 O4 c1cc(c(cc1....
78 5NHP ic50 = 0.023 uM 8XK C19 H23 N7 O2 Cn1c(ccn1)....
79 3I60 Ki < 2 nM E86 C24 H22 Cl N5 O2 Cc1cnc(nc1....
80 4XP2 - TT4 C8 H9 N5 c1ccc(cc1)....
81 1PME Ki = 0.76 nM SB2 C21 H16 F N3 O S C[S@](=O)c....
82 6Q7T - HOW C3 H4 N2 O c1conc1N
83 5NHL ic50 < 0.0003 uM 8XB C20 H25 N7 O2 Cc1cnc(nc1....
84 5HD4 - 38Z C33 H33 N9 O2 c1cnc(nc1)....
85 6G97 ic50 = 4.2 nM EQZ C20 H23 Cl N4 O3 COCCN1Cc2c....
86 6G92 ic50 = 76000 nM ERZ C10 H13 N5 Cc1cnc(nc1....
87 5K4I ic50 = 3.1 nM 6QB C21 H18 Cl F N6 O2 Cn1c(ccn1)....
70% Homology Family (90)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 10 families.
1 6GDM - F3Z C33 H33 N9 O2 c1cnc(nc1)....
2 4XP3 - DX4 C5 H5 N5 S c1[nH]c2c(....
3 6QAQ - HVQ C5 H8 N S c1cscc1C[N....
4 4O6E ic50 = 1 nM 2SH C21 H25 Cl F N5 O3 c1cc(c(cc1....
5 5NHJ ic50 < 0.0003 uM 8XE C18 H21 N7 O2 Cn1c(ccn1)....
6 4QYY Kd = 0.05 uM 3G7 C25 H29 Cl N4 O4 CC(=O)c1cc....
7 6QAG - HUH C2 H3 N3 c1cnn[nH]1
8 4I5H Ki < 2 nM G17 C26 H21 F3 N4 O Cc1ccc(cc1....
9 6G93 ic50 = 11 nM EU2 C17 H17 Cl N4 O2 c1cc2c(cc1....
10 4QTE Kd = 0.084 uM 390 C24 H20 Cl2 F N5 O2 Cc1cnc(nc1....
11 4XNE - TT4 C8 H9 N5 c1ccc(cc1)....
12 3QYW - 6PB C11 H8 Br N5 c1cc(cc(c1....
13 5BUE ic50 = 0.003 uM 4V8 C23 H21 N5 O c1ccc(cc1)....
14 6GE0 ic50 = 2.1 nM EVQ C28 H30 Cl N5 O4 C[C@H](c1c....
15 6G9N ic50 = 3 nM ESN C29 H32 Cl N5 O4 Cc1cccc(c1....
16 2Z7L - S91 C20 H19 N5 O3 Cc1cccc(c1....
17 6QAW - HVE C12 H18 N5 c1c[nH]c2c....
18 4ZXT - CAQ C6 H6 O2 c1ccc(c(c1....
19 1WZY ic50 = 0.56 uM F29 C21 H17 N7 C=CCn1c2c(....
20 6DMG - EK6 C27 H26 Cl2 F N5 O4 CCOC(=O)CN....
21 5NHH ic50 < 0.00113 uM 8XH C19 H25 N5 O3 COCCN1CCc2....
22 6OPH - 6QB C21 H18 Cl F N6 O2 Cn1c(ccn1)....
23 6G9H ic50 = 4 nM ERW C24 H30 Cl N5 O3 CC(C)(C)N(....
24 4N4S - 2H1 C25 H24 N6 O Cc1cc(cc2c....
25 4QP8 ic50 = 0.28 uM 362 C14 H10 N6 c1cc(cnc1)....
26 6SLG Kd = 0.00000145 M LHZ C24 H24 F2 N8 O2 Cc1cnc(nc1....
27 4QP4 - 36O C11 H15 N5 c1[nH]c2c(....
28 6G9D ic50 = 4.3 nM ER8 C23 H28 Cl N5 O3 CC(C)(C)NC....
29 6GJB ic50 = 0.008 uM F0H C35 H34 Cl F N6 O4 c1cc(c(cc1....
30 6G91 ic50 = 3200 nM EQW C9 H12 Cl N3 O c1c(cnc(n1....
31 6G8X - EQT C7 H6 Cl N3 c1cc2c(c(c....
32 6DCG ic50 = 7 nM G67 C37 H41 N9 O3 S CC(C)Oc1cc....
33 4QP9 ic50 = 0.071 uM 35X C17 H16 N6 CCCn1cc(cn....
34 5BVE ic50 = 0.01 nM 4VG C25 H28 Cl N5 O3 c1cc(cc(c1....
35 6Q7S - IPH C6 H6 O c1ccc(cc1)....
36 5KE0 - 6S9 C20 H18 N6 O Cc1cc(ccn1....
37 6CPW ic50 = 5.6 nM F8V C35 H35 F N8 O2 S CS[C@]1(CC....
38 4XOY - DX4 C5 H5 N5 S c1[nH]c2c(....
39 6G9K - ESK C27 H28 Cl N5 O4 c1ccc(cc1)....
40 3QYZ - Z8B C10 H11 Br N8 O3 c1nc(c2c(n....
41 5BVF ic50 = 0.19 nM 4VJ C25 H28 Cl N5 O3 c1cc(cc(c1....
42 6G9M ic50 = 7.9 nM ESW C28 H30 Cl N5 O3 CC(C)(c1cc....
43 6QAH - HVB C3 H9 N2 CCC(=[NH2+....
44 6QA3 - PZO C3 H4 N2 c1c[nH]nc1
45 4XOZ - 620 C15 H16 N6 O c1ccc(cc1)....
46 5HD7 - 38Z C33 H33 N9 O2 c1cnc(nc1)....
47 4XRJ - 620 C15 H16 N6 O c1ccc(cc1)....
48 2OJJ Ki = 0.002 uM 82A C22 H17 Cl2 F N4 O2 c1cc(cc(c1....
49 6Q7K - 2AI C3 H5 N3 c1cnc([nH]....
50 4QTA Kd = 0.013 uM 38Z C33 H33 N9 O2 c1cnc(nc1)....
51 6RQ4 - KE8 C22 H27 N7 O2 S CC1(c2c(cc....
52 5NHO ic50 < 0.0003 uM 8XN C20 H25 N7 O2 Cc1cnc(nc1....
53 2OJG Ki = 2.3 uM 19A C16 H16 N4 O CN(C)C(=O)....
54 4XP0 - 42A C8 H5 N3 c1cc2c(c[n....
55 4QP2 Kd = 940 uM 36R C7 H5 Cl N2 O c1cc2c(cc1....
56 5NHF ic50 = 0.0012 uM 8X5 C23 H25 N5 O2 c1ccc(cc1)....
57 5BUJ ic50 = 0.005 uM 4VB C16 H15 N5 O c1cnccc1c2....
58 6G9J ic50 = 4.1 nM ERK C27 H28 Cl N5 O3 C[C@H](c1c....
59 5BUI ic50 = 0.089 uM 4V9 C17 H15 F N4 c1ccnc(c1)....
60 4QP7 ic50 = 5.9 uM 363 C9 H7 N5 c1c[nH]c2c....
61 3ERK ic50 = 18 uM SB4 C18 H19 F N6 c1cc(ccc1c....
62 6GDQ - EVK C21 H22 Cl2 N4 O2 CC(C)Nc1cc....
63 5V60 - ACP C11 H18 N5 O12 P3 c1nc(c2c(n....
64 6QA1 - HVK C5 H6 N2 c1ccnc(c1)....
65 1TVO Ki = 0.14 uM FRZ C18 H13 N7 c1ccc(cc1)....
66 6G9A ic50 = 21 nM ESQ C23 H28 Cl N5 O3 c1cc2c(cc1....
67 5BVD ic50 = 0.16 nM 4VF C24 H26 Cl N5 O3 c1cc(cc(c1....
68 4ZZN ic50 = 0.26 uM CQ8 C18 H21 Cl N4 O2 CNC(=O)c1c....
69 3SA0 - NRA C13 H8 O6 c1c(cc2c(c....
70 4ERK ic50 = 27 uM OLO C15 H18 N6 O Cn1cnc2c1n....
71 6GJD ic50 = 0.022 uM F0E C46 H55 N11 O5 c1cnc(nc1)....
72 5U6I - 81Y C19 H22 N4 O2 CC(C)Oc1cc....
73 5NHV ic50 = 0.0028 uM 8QB C16 H19 N5 O2 c1cnc(nc1c....
74 6QAL - HV2 C3 H6 O3 S C1C(CS1(=O....
75 3I5Z Ki = 2 nM Z48 C24 H23 N5 O2 Cc1cnc(nc1....
76 6QA4 - HRZ C5 H5 N O C1=CC(=O)N....
77 4N0S - DHC C9 H8 O4 c1cc(c(cc1....
78 5NHP ic50 = 0.023 uM 8XK C19 H23 N7 O2 Cn1c(ccn1)....
79 3I60 Ki < 2 nM E86 C24 H22 Cl N5 O2 Cc1cnc(nc1....
80 4XP2 - TT4 C8 H9 N5 c1ccc(cc1)....
81 1PME Ki = 0.76 nM SB2 C21 H16 F N3 O S C[S@](=O)c....
82 6Q7T - HOW C3 H4 N2 O c1conc1N
83 5NHL ic50 < 0.0003 uM 8XB C20 H25 N7 O2 Cc1cnc(nc1....
84 5HD4 - 38Z C33 H33 N9 O2 c1cnc(nc1)....
85 6G97 ic50 = 4.2 nM EQZ C20 H23 Cl N4 O3 COCCN1Cc2c....
86 6G92 ic50 = 76000 nM ERZ C10 H13 N5 Cc1cnc(nc1....
87 5K4I ic50 = 3.1 nM 6QB C21 H18 Cl F N6 O2 Cn1c(ccn1)....
88 4QTB Kd = 0.084 uM 38Z C33 H33 N9 O2 c1cnc(nc1)....
89 2ZOQ ic50 = 0.9 uM 5ID C11 H13 I N4 O4 c1c(c2c(nc....
90 6GES - EWH C24 H26 Cl N7 O CN1CCN(CC1....
50% Homology Family (9)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 7 families.
1 6GDM - F3Z C33 H33 N9 O2 c1cnc(nc1)....
2 4XP3 - DX4 C5 H5 N5 S c1[nH]c2c(....
3 6QAQ - HVQ C5 H8 N S c1cscc1C[N....
4 3GCV Kd = 74 nM SS6 C29 H30 N8 O Cc1cccc(c1....
5 3L8S Kd = 99 nM BFF C20 H24 Br F2 N5 O3 S c1c(cc(c(c....
6 3RIN ic50 = 1.3 nM I2O C23 H24 N2 O2 Cc1ccc(cc1....
7 5N65 - 8OT C20 H18 N4 S c1ccc(cc1)....
8 4H3B Kd = 17.2 uM VAL VAL ARG PRO GLY SER LEU ASP LEU PRO n/a n/a
9 4ZSL - 4QZ C17 H17 Cl N6 O C[C@@H](c1....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: F3Z; Similar ligands found: 5
No: Ligand ECFP6 Tc MDL keys Tc
1 F3Z 1 1
2 38Z 0.711864 1
3 F0E 0.652778 0.835616
4 F8V 0.544776 0.824324
5 3G7 0.459677 0.716216
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 5BVE; Ligand: 4VG; Similar sites found with APoc: 27
This union binding pocket(no: 1) in the query (biounit: 5bve.bio1) has 70 residues
No: Leader PDB Ligand Sequence Similarity
1 6JKM ADP 20.5279
2 6AC9 ANP 24.9307
3 2F2U M77 26.3158
4 2F2U M77 26.3158
5 3DLS ADP 26.5672
6 3DLS ADP 26.5672
7 5DBX ANP 30.1829
8 4Y8D 49J 30.2941
9 5HVJ ANP 30.4762
10 6F3G CJN 33.2203
11 2A19 ANP 34.507
12 4DC2 ADE 34.903
13 3DAK ANP 35.1724
14 3DAK ANP 35.1724
15 5UPK ANP 38.4393
16 1Q8Y ADE 39.0582
17 6U5L 3RJ 40.0697
18 6P5S 3NG 40.4432
19 2V7O DRN 41.9643
20 2WEL K88 42.8135
21 5Y86 HRM 44.0443
22 2VZ6 FEF 44.4089
23 4C2W ANP 45.8781
24 4NST AF3 46.4387
25 2VN9 GVD 46.5116
26 2VN9 GVD 46.5116
27 2ZV2 609 48.3221
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