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Receptor
PDB id Resolution Class Description Source Keywords
5EHR 1.7 Å EC: 3.1.3.48 NON-RECEPTOR PROTEIN TYROSINE PHOSPHATASE SHP2 IN COMPLEX WI ALLOSTERIC INHIBITOR SHP099 HOMO SAPIENS PHOSPHATASE PTP INHIBITOR PTPN11 ALLOSTERIC HYDROLASE-HYDROINHIBITOR COMPLEX
Ref.: ALLOSTERIC INHIBITION OF SHP2 PHOSPHATASE INHIBITS DRIVEN BY RECEPTOR TYROSINE KINASES. NATURE V. 535 148 2016
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
PO4 B:603;
A:604;
A:602;
A:603;
B:602;
B:604;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
none;
none;
none;
none;
none;
none;
submit data
94.971 O4 P [O-]P...
5OD A:601;
B:601;
Valid;
Valid;
none;
none;
Kd = 73 nM
352.262 C16 H19 Cl2 N5 CC1(C...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
5EHR 1.7 Å EC: 3.1.3.48 NON-RECEPTOR PROTEIN TYROSINE PHOSPHATASE SHP2 IN COMPLEX WI ALLOSTERIC INHIBITOR SHP099 HOMO SAPIENS PHOSPHATASE PTP INHIBITOR PTPN11 ALLOSTERIC HYDROLASE-HYDROINHIBITOR COMPLEX
Ref.: ALLOSTERIC INHIBITION OF SHP2 PHOSPHATASE INHIBITS DRIVEN BY RECEPTOR TYROSINE KINASES. NATURE V. 535 148 2016
Members (10)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 28 families.
1 6BMU - DZV C23 H17 Cl N4 O3 COc1cccc(c....
2 6BMX - DYV C29 H24 Cl N5 O6 COc1cccc(c....
3 6BMV - DZS C23 H15 Cl N4 O4 c1ccc(c(c1....
4 6BN5 - DZJ C17 H11 Cl N2 O2 S c1ccc(cc1)....
5 6BMY - DYV C29 H24 Cl N5 O6 COc1cccc(c....
6 5EHR Kd = 73 nM 5OD C16 H19 Cl2 N5 CC1(CCN(CC....
7 6BMW - DZS C23 H15 Cl N4 O4 c1ccc(c(c1....
8 6BMR - DZV C23 H17 Cl N4 O3 COc1cccc(c....
9 6CMR - 5OD C16 H19 Cl2 N5 CC1(CCN(CC....
10 5EHP ic50 = 12 uM 5OA C16 H19 Cl2 N5 C[C@@H]1CN....
70% Homology Family (10)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 26 families.
1 6BMU - DZV C23 H17 Cl N4 O3 COc1cccc(c....
2 6BMX - DYV C29 H24 Cl N5 O6 COc1cccc(c....
3 6BMV - DZS C23 H15 Cl N4 O4 c1ccc(c(c1....
4 6BN5 - DZJ C17 H11 Cl N2 O2 S c1ccc(cc1)....
5 6BMY - DYV C29 H24 Cl N5 O6 COc1cccc(c....
6 5EHR Kd = 73 nM 5OD C16 H19 Cl2 N5 CC1(CCN(CC....
7 6BMW - DZS C23 H15 Cl N4 O4 c1ccc(c(c1....
8 6BMR - DZV C23 H17 Cl N4 O3 COc1cccc(c....
9 6CMR - 5OD C16 H19 Cl2 N5 CC1(CCN(CC....
10 5EHP ic50 = 12 uM 5OA C16 H19 Cl2 N5 C[C@@H]1CN....
50% Homology Family (132)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 16 families.
1 1L8G - DBD C18 H14 N2 O9 S2 c1ccc2c(c1....
2 2CNI ic50 = 21 nM IZF C31 H34 Cl N3 O10 S2 COC(=O)c1c....
3 2F6Y ic50 = 134.8 uM ENT C16 H23 N3 O6 S CC(C)(C)OC....
4 2F6T Ki = 24 uM 1C2 C16 H23 N3 O6 S CC(C)(C)OC....
5 1NL9 - 989 C29 H31 N3 O7 CCCCCNC(=O....
6 2CM7 ic50 = 210 nM IZD C23 H26 N4 O6 S CC(=O)N[C@....
7 1C83 Ki = 14 uM OAI C11 H8 N2 O5 c1c[nH]c2c....
8 2AZR Ki = 230 uM 982 C10 H7 N O5 S c1cc2c(c(s....
9 1PH0 - 418 C34 H35 N3 O12 COC(=O)c1c....
10 1Q6N ic50 = 0.023 uM P90 C31 H25 F2 N4 O3 P S c1ccc(cc1)....
11 1Q6S ic50 = 12 nM 214 C38 H32 F2 N4 O6 P2 Cc1ccc2cc(....
12 1KAK ic50 = 26 uM FNP C12 H10 F4 O6 P2 c1cc(cc2c1....
13 2HB1 Ki = 160 uM 512 C7 H5 Br O5 S c1c(c(c(s1....
14 1PTV - PTR C9 H12 N O6 P c1cc(ccc1C....
15 1BZH Ki = 0.17 uM ASP ALA ASP GLU FLT LEU AEA n/a n/a
16 2CNE ic50 = 1.7 nM DFJ C28 H29 F4 N3 O9 P2 c1ccc(cc1)....
17 1XBO Ki = 6.9 uM IX1 C22 H19 N O8 COC(=O)c1c....
18 2F6Z ic50 = 4.8 uM UN5 C20 H24 N4 O8 S2 CNC(=O)[C@....
19 2CMA ic50 = 185 nM F20 C28 H28 N4 O6 S c1ccc(cc1)....
20 1PTY - PTR C9 H12 N O6 P c1cc(ccc1C....
21 1C88 Ki = 5.1 uM OTA C10 H10 N2 O5 S C1CNCc2c1c....
22 1ECV Ki = 14 uM 878 C9 H6 I N O5 c1cc(c(cc1....
23 2F6V ic50 = 37 uM SK2 C19 H21 N3 O6 S CNC(=O)[C@....
24 2CNF ic50 = 240 nM F32 C25 H21 N5 O3 S2 c1ccc2c(c1....
25 1ONZ - 968 C19 H13 N O6 c1ccc(c(c1....
26 2QBS Ki = 0.21 uM 024 C19 H20 Br N O5 S c1cc(cc(c1....
27 2VEV ic50 = 1300 nM IZ2 C28 H25 F3 N4 O5 S2 c1ccc(cc1)....
28 4Y14 Ki = 40 nM C0A C12 H16 Br F2 N2 O6 P S CNC(=O)[C@....
29 1ONY - 588 C27 H32 N4 O9 S CCCCCNC(=O....
30 1NNY - 515 C40 H37 N3 O10 CC(=O)N[C@....
31 2ZN7 Kd = 13 nM 410 C26 H24 Br N O6 S c1ccc(cc1)....
32 2VEU ic50 = 2900 nM IZ1 C27 H23 F3 N4 O5 S2 c1ccc(cc1)....
33 1JF7 - TBH C31 H47 N3 O9 CCCCCN[C@@....
34 5KAD Kd = 37 uM OTA C10 H10 N2 O5 S C1CNCc2c1c....
35 5KA3 Kd = 26 uM OTA C10 H10 N2 O5 S C1CNCc2c1c....
36 3EAX Ki = 12 uM LZP C38 H34 N2 O8 c1ccc(cc1)....
37 1QXK Ki ~ 9 uM 429 C25 H30 N2 O10 CC(=O)N[C@....
38 2QBR Ki = 0.47 uM 910 C20 H16 Br N O5 S c1ccc(cc1)....
39 1T48 ic50 = 350 uM BB3 C19 H17 Br2 N O5 S CCc1c(c2cc....
40 1PYN Ki = 3.2 uM 941 C29 H36 N2 O12 CC(C)(C)OC....
41 2FJN ic50 = 39 nM 073 C32 H28 F2 N3 O5 P COC(=O)c1c....
42 2F71 ic50 = 2.5 uM UN7 C21 H23 N3 O7 S CNC(=O)[C@....
43 1Q6P ic50 = 3 nM 213 C34 H29 F2 N3 O6 P2 c1ccc(cc1)....
44 1WAX ic50 = 86 uM LO1 C9 H10 N2 O3 c1cc(ccc1C....
45 2CNH ic50 = 59 nM IZB C27 H27 N5 O6 S2 CN1CCOc2c1....
46 1Q6T ic50 = 7 nM 600 C43 H42 F2 N4 O7 P2 CC(C)C[C@@....
47 2VEX ic50 = 130 nM IZ4 C28 H29 F N4 O5 S2 c1ccc(cc1)....
48 1Q6J ic50 = 0.016 uM 335 C29 H25 F4 N3 O6 P2 c1ccc(cc1)....
49 3EB1 Ki = 16 uM LZQ C24 H21 N O4 c1ccc(cc1)....
50 1G7F Ki = 3.4 uM INZ C27 H33 N3 O9 CCCCCNC(=O....
51 2ZMM Ki = 25 nM 35B C21 H23 Br N2 O6 S CNC(=O)N(c....
52 1AAX - BPM C13 H14 O8 P2 c1cc(ccc1C....
53 1BZC Ki = 12 uM TPI C17 H17 F2 N2 O7 P c1cc(cc2c1....
54 2QBQ Ki = 0.036 uM 4B3 C23 H28 Br N O5 S CC1(CC(CC(....
55 5K9W Kd = 26 uM OTA C10 H10 N2 O5 S C1CNCc2c1c....
56 6B8Z - FRJ C26 H19 Br2 N3 O7 S3 CCc1c(c2cc....
57 2CMC ic50 = 1750 nM DFM C21 H24 F2 N3 O6 P CC(=O)N[C@....
58 2CMB ic50 = 65 nM F17 C32 H29 N5 O9 S2 c1ccc(cc1)....
59 2F70 ic50 = 33.5 uM UN6 C16 H19 N3 O7 S2 c1cc(cc(c1....
60 1KAV Ki = 1.5 uM FEP C18 H20 F4 O6 P2 c1cc(ccc1C....
61 2NT7 Ki = 0.3 uM 902 C25 H25 Br N6 O5 S2 c1ccc(cc1)....
62 1C87 Ki = 63 uM OPA C10 H9 N O6 S C1COCc2c1c....
63 5KAB - OTA C10 H10 N2 O5 S C1CNCc2c1c....
64 2H4K Ki = 3.2 uM 509 C13 H9 Br O5 S c1ccc(cc1)....
65 1G7G Ki = 0.25 uM INX C30 H37 N3 O10 CCCCCNC(=O....
66 5T19 - 73U C16 H17 N3 O3 S Cc1ccc(cc1....
67 1C86 Ki = 20 uM OPA C10 H9 N O6 S C1COCc2c1c....
68 2H4G Ki = 0.3 uM 694 C13 H9 Br O6 S c1cc(ccc1c....
69 5KA1 Kd = 33 uM OTA C10 H10 N2 O5 S C1CNCc2c1c....
70 2BGE ic50 = 1608 uM T2D C8 H8 N2 O3 S c1ccc(cc1)....
71 1PXH - SNA C32 H41 F4 N5 O13 P2 S c1cc(ccc1C....
72 2QBP Ki = 0.004 uM 527 C25 H25 Br N2 O7 S2 c1ccc(cc1)....
73 1Q6M ic50 = 0.013 uM P27 C29 H23 F6 N3 O6 P2 c1ccc2c(c1....
74 2VEW ic50 = 64 nM IZ3 C27 H22 F2 N4 O5 S2 c1ccc(c(c1....
75 2B07 Ki = 0.37 uM 598 C25 H24 N2 O7 S3 c1ccc(cc1)....
76 3I7Z - ASP ALA ASP GLU TYR LEU n/a n/a
77 1EEN - ALA ASP PBF PTR LEU ILE PRO n/a n/a
78 1LQF - BGD C32 H34 F4 N4 O12 P2 c1ccc(cc1)....
79 2BGD ic50 = 2.47 uM T1D C15 H14 N2 O4 S COc1ccc(cc....
80 1T49 ic50 = 22 uM 892 C23 H18 Br2 N2 O7 S2 CCc1c(c2cc....
81 2NTA Ki = 16 uM 521 C12 H9 Cl N2 O3 S2 c1ccc(cc1)....
82 1NWL - 964 C19 H27 N5 O5 S2 CC(=O)NCCS....
83 2VEY ic50 = 43 nM IZ5 C29 H29 F N4 O5 S2 c1ccc(cc1)....
84 5KA7 Kd = 45 uM OTA C10 H10 N2 O5 S C1CNCc2c1c....
85 2FJM ic50 = 142 nM 073 C32 H28 F2 N3 O5 P COC(=O)c1c....
86 1GFY - COL C10 H9 N O5 S2 C1CSCc2c1c....
87 1NZ7 - 901 C32 H40 N4 O10 S CCc1cc(ccc....
88 3CWE ic50 = 0.12 uM 825 C22 H18 Br F2 O4 P c1ccc(cc1)....
89 2CNG ic50 = 110 nM IZE C21 H16 F6 N4 O4 S c1cc(ccc1C....
90 2CM8 ic50 = 1350 nM F16 C9 H7 N O4 S c1cc(cc(c1....
91 1BZJ Ki = 22 uM PIC C12 H9 F2 O5 P c1cc(cc2c1....
92 2F6W - UN3 C10 H11 N3 O3 S Cn1c(cc(n1....
93 1NO6 - 794 C19 H13 N O5 c1ccc2c(c1....
94 1C84 Ki = 9.9 uM 761 C13 H9 N O5 c1ccc2cc(c....
95 5KA9 Kd = 39 uM OTA C10 H10 N2 O5 S C1CNCc2c1c....
96 4GE6 ic50 = 75 nM B26 C42 H45 Br F2 I N6 O11 P Cc1cc(ccc1....
97 4GE5 ic50 = 0.27 uM A89 C30 H31 Br F2 I N4 O7 P Cc1cc(ccc1....
98 4GE2 ic50 = 0.9 uM 75A C24 H28 F2 I N4 O7 P CC(=O)N[C@....
99 3D44 - LEU ASP GLU PTR VAL ALA THR ARG n/a n/a
100 3D42 - LEU THR GLU PTR VAL ALA THR ARG n/a n/a
101 3O5X ic50 = 5.5 uM JZG C33 H27 N5 O4 Cn1c2cc(c(....
102 4RDD ic50 = 16.8 uM 3LU C21 H22 N3 O8 S2 c1ccc(cc1)....
103 4RH5 Kd = 127.3 nM PHE SER ALA PTR PRO SER GLU GLU ASP n/a n/a
104 6BMU - DZV C23 H17 Cl N4 O3 COc1cccc(c....
105 6BMX - DYV C29 H24 Cl N5 O6 COc1cccc(c....
106 6BMV - DZS C23 H15 Cl N4 O4 c1ccc(c(c1....
107 6BN5 - DZJ C17 H11 Cl N2 O2 S c1ccc(cc1)....
108 6BMY - DYV C29 H24 Cl N5 O6 COc1cccc(c....
109 5EHR Kd = 73 nM 5OD C16 H19 Cl2 N5 CC1(CCN(CC....
110 6BMW - DZS C23 H15 Cl N4 O4 c1ccc(c(c1....
111 6BMR - DZV C23 H17 Cl N4 O3 COc1cccc(c....
112 6CMR - 5OD C16 H19 Cl2 N5 CC1(CCN(CC....
113 5EHP ic50 = 12 uM 5OA C16 H19 Cl2 N5 C[C@@H]1CN....
114 3QCH ic50 = 3.3 uM NX2 C13 H11 Cl2 N O3 S3 CS(=O)(=O)....
115 3QCI ic50 = 3.8 uM NX3 C18 H14 Cl2 N2 O3 S3 c1cc(cc(c1....
116 3QCJ ic50 = 0.5 uM NX4 C20 H15 Cl2 N O6 S3 COc1ccc(cc....
117 3QCL ic50 = 4 uM NXV C18 H14 Cl2 O3 S c1cc(c(cc1....
118 3QCE ic50 = 6.6 uM NXY C12 H8 Cl2 O2 S2 c1cc(c(cc1....
119 3QCM - NXW C27 H25 Cl2 N3 O3 S CNCCNCC(=O....
120 3QCF ic50 = 6.6 uM NXY C12 H8 Cl2 O2 S2 c1cc(c(cc1....
121 3QCG - NX1 C12 H8 Br Cl O2 S2 c1cc(c(cc1....
122 3QCK ic50 = 5.8 uM NX5 C14 H10 Cl2 O2 S c1ccc(c(c1....
123 5OVX Ki = 7.8 uM AY5 C20 H17 Cl2 O5 P c1cc(cc(c1....
124 6H8R - FWB C10 H12 F3 N O C[C@@H](Cc....
125 5OW1 Ki = 20 uM AY8 C19 H21 F2 O4 P c1cc(cc(c1....
126 4J51 ic50 = 259 nM N75 C28 H20 Cl N O6 c1cc(cc(c1....
127 2I5X - UA5 C8 H11 N O3 S CCc1ccc(cc....
128 2I4H - UA1 C24 H32 N4 O8 S CC(C)(C)OC....
129 2H02 ic50 = 0.32 uM 2UN C19 H21 N O7 S COC(=O)C(C....
130 2I4G - UA1 C24 H32 N4 O8 S CC(C)(C)OC....
131 2H04 ic50 = 0.07 uM 4UN C21 H21 N5 O5 S Cc1nc(no1)....
132 2H03 ic50 = 0.09 uM 3UN C21 H32 N2 O9 S CCOC(=O)C(....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: 5OD; Similar ligands found: 1
No: Ligand ECFP6 Tc MDL keys Tc
1 5OD 1 1
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 5EHR; Ligand: 5OD; Similar sites found with APoc: 81
This union binding pocket(no: 1) in the query (biounit: 5ehr.bio2) has 21 residues
No: Leader PDB Ligand Sequence Similarity
1 4WG0 CHD None
2 1ZEI CRS None
3 5ZYN FMN 1.27389
4 6A0S NDP 1.50602
5 4ARE FLC 1.52091
6 5LX9 OLB 1.76056
7 1ZPD CIT 1.90114
8 4WOE 3S5 1.90114
9 1GEG GLC 1.95312
10 4RW3 TDA 1.98676
11 6CB2 OLC 2.04778
12 2UW1 GVM 2.66272
13 1W3T 3GR 2.72109
14 3P9T TCL 2.73973
15 4U03 TLL 2.8103
16 4U03 GTP 2.8103
17 3AQT RCO 2.85714
18 6HL7 CP 2.87356
19 5XJ7 87O 2.98507
20 4RJD TFP 3.0303
21 1M2Z BOG 3.11284
22 4G8R 96P 3.19149
23 3G58 988 3.41207
24 4DXJ 0M9 3.59116
25 3WMX THR 3.63128
26 1Q3A NGH 3.63636
27 5D9J 0N8 3.74332
28 4DO1 ANN 3.90244
29 1EYQ NAR 4.05405
30 2E2R 2OH 4.09836
31 4K10 NI9 4.14365
32 1ZED PNP 4.33884
33 2GWH PCI 4.36242
34 3G5K BB2 4.37158
35 3TL1 JRO 4.40252
36 1XMY ROL 4.52261
37 3O01 DXC 4.54545
38 3N2O AG2 4.56274
39 5IM3 DTP 4.56274
40 6CS8 F9Y 4.9505
41 1XQP 8HG 5.07812
42 4UCC ZKW 5.15021
43 2JC9 ADN 5.51331
44 3RV5 DXC 5.61798
45 5CX6 CDP 5.70342
46 4MGA 27L 5.88235
47 5LWY OLB 6.54206
48 4PB2 5UD 6.83962
49 3ZVS MLI 6.875
50 2VWA PTY 6.93069
51 6CGN DA 7.03422
52 1XVB 3BR 7.05882
53 1XVB BHL 7.05882
54 3SFI 3SF 7.20339
55 4F06 PHB 7.27763
56 5UGW GSH 8
57 1NU4 MLA 8.24742
58 5W7B MYR 8.51064
59 2YFB SIN 8.52713
60 1R6N 434 8.53081
61 2WOR 2AN 9
62 4UMJ BFQ 9.12162
63 5EXA 5SO 9.56522
64 5OCA 9QZ 10.3175
65 3KYF 5GP 5GP 11.2554
66 2GBB CIT 11.5385
67 3MG9 GHP 3MY 3FG GHP GHP OMY 3FG 11.5646
68 3W5N RAM 12.3574
69 3N7S 3N7 12.5
70 3KP6 SAL 12.5828
71 4OGQ 7PH 13.4078
72 4ZGM 32M 13.9344
73 2Y69 CHD 15
74 2BCG GER 15.0485
75 5C9J DAO 18.1818
76 3KO0 TFP 18.8119
77 5ZCO CHD 21.4286
78 5Z84 CHD 21.4286
79 5W97 CHD 21.4286
80 5NNT DPV 21.6216
81 5V4R MGT 28.3951
Pocket No.: 2; Query (leader) PDB : 5EHR; Ligand: 5OD; Similar sites found with APoc: 4
This union binding pocket(no: 2) in the query (biounit: 5ehr.bio1) has 24 residues
No: Leader PDB Ligand Sequence Similarity
1 4WGF HX2 5.85366
2 5F4B FMN 7.42574
3 4OGQ 2WD 13.4078
4 2ALG DAO 17.3913
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