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Receptor
PDB id Resolution Class Description Source Keywords
5FWJ 2.1 Å EC: 1.14.11.- CRYSTAL STRUCTURE OF HUMAN JARID1C IN COMPLEX WITH KDM5-C49 HOMO SAPIENS OXIDOREDUCTASE LYSINE-SPECIFIC LYSINE-SPECIFIC DEMETHYLASE
Ref.: STRUCTURAL ANALYSIS OF HUMAN KDM5B GUIDES HISTONE DEMETHYLASE INHIBITOR DEVELOPMENT. NAT.CHEM.BIOL. V. 12 539 2016
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
MMK B:1775;
A:1775;
Valid;
Valid;
none;
none;
Ki = 0.0061 uM
306.36 C15 H22 N4 O3 CCN(/...
MN A:1772;
B:1772;
Part of Protein;
Part of Protein;
none;
none;
submit data
54.938 Mn [Mn+2...
MG A:1773;
A:805;
B:1774;
A:1774;
B:1773;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
none;
none;
none;
none;
none;
submit data
24.305 Mg [Mg+2...
ZN A:1770;
B:1770;
A:1771;
B:1771;
Invalid;
Invalid;
Invalid;
Invalid;
none;
none;
none;
none;
submit data
65.409 Zn [Zn+2...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
5FWJ 2.1 Å EC: 1.14.11.- CRYSTAL STRUCTURE OF HUMAN JARID1C IN COMPLEX WITH KDM5-C49 HOMO SAPIENS OXIDOREDUCTASE LYSINE-SPECIFIC LYSINE-SPECIFIC DEMETHYLASE
Ref.: STRUCTURAL ANALYSIS OF HUMAN KDM5B GUIDES HISTONE DEMETHYLASE INHIBITOR DEVELOPMENT. NAT.CHEM.BIOL. V. 12 539 2016
Members (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 31 families.
1 5FWJ Ki = 0.0061 uM MMK C15 H22 N4 O3 CCN(/C=C/N....
70% Homology Family (10)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 19 families.
1 5FWJ Ki = 0.0061 uM MMK C15 H22 N4 O3 CCN(/C=C/N....
2 5A3N ic50 = 19 nM LQT C15 H25 N5 O2 CCN(CCN(C)....
3 5A3W Ki = 0.39 uM PD2 C7 H5 N O4 c1cnc(cc1C....
4 5FPL - MN QAY n/a n/a
5 5FPU Ki = 0.14 uM K0I C22 H23 N5 O2 c1ccc2c(c1....
6 5FUP - AKG C5 H6 O5 C(CC(=O)O)....
7 5FV3 Ki = 6.32 uM OGA C4 H5 N O5 C(C(=O)O)N....
8 5A1F Ki = 6.32 uM OGA C4 H5 N O5 C(C(=O)O)N....
9 5FUN Ki = 0.01 uM GZA C17 H13 N5 O2 c1ccc(cc1)....
10 5A3T Ki = 0.001 uM MMK C15 H22 N4 O3 CCN(/C=C/N....
50% Homology Family (40)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1 families.
1 5FWJ Ki = 0.0061 uM MMK C15 H22 N4 O3 CCN(/C=C/N....
2 5IVE Kd = 0.027 uM 6E8 C11 H12 N4 O CC1=C(C(=O....
3 6DQA - H6V C22 H25 N3 O3 S c1cc(cc(c1....
4 6BGX Kd = 0.47 uM DKV C22 H21 Cl F2 N2 O3 c1ccc(c(c1....
5 6BGV Kd = 0.18 uM DQG C22 H24 Cl N3 O3 c1ccc(c(c1....
6 5IVY Kd = 0.36 uM 6EO C14 H11 Cl N2 O3 c1cc(ccc1C....
7 6DQ5 Kd = 6 uM H6G C20 H24 N6 O3 C=CC(=O)N1....
8 6DQ8 Kd = 0.26 uM H6S C22 H23 Cl N2 O3 S CN1CCC[C@H....
9 5IWF - LQT C15 H25 N5 O2 CCN(CCN(C)....
10 5IVC Kd = 1.2 uM 6E7 C20 H17 N3 O3 c1ccc(cc1)....
11 6BH2 Kd = 2.4 uM 90V C15 H22 N4 O2 CC(C)c1cc(....
12 5IVV Kd = 0.45 uM 6EN C14 H12 N4 O2 Cn1cc(c2c1....
13 5ISL Kd = 0.052 uM MMK C15 H22 N4 O3 CCN(/C=C/N....
14 6BH5 Kd = 0.25 uM DNY C23 H26 Cl N3 O3 c1ccc(c(c1....
15 5E6H Kd = 79 uM AKG C5 H6 O5 C(CC(=O)O)....
16 6BGU Kd = 0.53 uM DKP C18 H17 Cl N2 O3 CCCO[C@H](....
17 6DQ6 Kd = 9 uM H6J C19 H24 N6 O4 S C=CS(=O)(=....
18 6BH1 Kd = 0.06 uM DQG C22 H24 Cl N3 O3 c1ccc(c(c1....
19 6DQ4 Kd = 12 uM K0I C22 H23 N5 O2 c1ccc2c(c1....
20 5IW0 Kd = 0.06 uM 6EP C17 H14 Cl N3 O3 Cc1cc(ccc1....
21 6BGY Kd = 0.15 uM DLJ C22 H24 Cl N3 O3 CN1CCC[C@@....
22 5IVJ Kd = 0.046 uM 6ED C20 H20 F3 N5 O2 c1cc2c(cc1....
23 6BH4 - DQS C17 H20 N6 O CC(C)C1=C(....
24 5IVB - AKG C5 H6 O5 C(CC(=O)O)....
25 5IVF - 6EB C15 H14 F3 N5 O2 Cn1cc(nc1)....
26 6BH0 Kd = 0.22 uM DO1 C22 H24 Cl N3 O3 c1ccc(c(c1....
27 6BGZ Kd = 0.41 uM DNV C21 H19 Cl N4 O3 Cn1ccnc1CC....
28 6BH3 - DQJ C15 H22 N4 O2 CC(C)c1cc(....
29 6BGW Kd = 0.21 uM DKS C22 H22 Cl F2 N3 O3 c1ccc(c(c1....
30 5A3N ic50 = 19 nM LQT C15 H25 N5 O2 CCN(CCN(C)....
31 5A3W Ki = 0.39 uM PD2 C7 H5 N O4 c1cnc(cc1C....
32 5FPL - MN QAY n/a n/a
33 5FPU Ki = 0.14 uM K0I C22 H23 N5 O2 c1ccc2c(c1....
34 5FUP - AKG C5 H6 O5 C(CC(=O)O)....
35 5FV3 Ki = 6.32 uM OGA C4 H5 N O5 C(C(=O)O)N....
36 5A1F Ki = 6.32 uM OGA C4 H5 N O5 C(C(=O)O)N....
37 5FUN Ki = 0.01 uM GZA C17 H13 N5 O2 c1ccc(cc1)....
38 5A3T Ki = 0.001 uM MMK C15 H22 N4 O3 CCN(/C=C/N....
39 4IGQ - OGA C4 H5 N O5 C(C(=O)O)N....
40 4IGO - AKG C5 H6 O5 C(CC(=O)O)....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: MMK; Similar ligands found: 2
No: Ligand ECFP6 Tc MDL keys Tc
1 MMK 1 1
2 LQT 0.466667 0.796296
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 5FWJ; Ligand: MMK; Similar sites found with APoc: 138
This union binding pocket(no: 1) in the query (biounit: 5fwj.bio1) has 15 residues
No: Leader PDB Ligand Sequence Similarity
1 4K3H 1OM None
2 2OVW CBI 0.973236
3 1RYD GLC 1.29199
4 5OCS FMN 1.61725
5 4OJ8 AKG 1.70648
6 4OJ8 2TQ 1.70648
7 3A5Y KAA 1.73913
8 6HTO 5AD 1.75
9 6HTO MET 1.75
10 4U98 ACP 1.76211
11 1NX4 AKG 1.8315
12 2NVA PL2 1.88172
13 4WCX MET 1.91083
14 5LUN OGA 1.98864
15 5LUN ARG 1.98864
16 2RKV COA 1.99557
17 3ZDS HQ9 2.07852
18 3KV5 OGA 2.12314
19 5C5H 4YB 2.20751
20 3KV4 OGA 2.23714
21 4J4H NAI 2.3166
22 4J4H 1J1 2.3166
23 2J3M ATP 2.33546
24 2J3M PRI 2.33546
25 3ETG NDP 2.33546
26 3ETG GLU 2.33546
27 4TW7 37K 2.34375
28 1ODM ASV 2.41692
29 3H7J PPY 2.46914
30 3MTX PGT 2.64901
31 3PUR 2HG 2.76008
32 3N9P OGA 2.76008
33 3N9Q OGA 2.76008
34 4P42 PEE 2.76008
35 3N9O OGA 2.76008
36 1UNB AKG 2.89389
37 1UNB PN1 2.89389
38 6GVZ CHO 2.95082
39 5NCJ SIN 2.98507
40 4CCK OGA 2.99786
41 4Y3O OGA 3.00429
42 1EP2 ORO 3.06513
43 1J3R 6PG 3.15789
44 1OS7 TAU 3.18021
45 1OS7 AKG 3.18021
46 5Y72 DST 3.28358
47 3FW4 CAQ 3.37079
48 4ZXA H8N 3.53982
49 5UQD AKG 3.61991
50 5HV0 AKG 3.68664
51 5JWP AKG 3.69318
52 3P3N AKG 3.72493
53 1H2M OGA 3.72493
54 1H2K OGA 3.72493
55 2WA4 069 3.72493
56 3NNF AKG 3.77907
57 4RF7 ARG 3.82166
58 2FCU AKG 3.83387
59 4YRD 3IT 3.89972
60 3N0Y APC 3.91061
61 2TPS TPS 3.96476
62 5L9V OGA 3.96825
63 5JSP DQY 3.9801
64 5TFZ 7BC 4
65 4WOE ADP 4.03397
66 4IQY AR6 4.16667
67 2RG0 CTT 4.18605
68 3E9I XAH 4.24628
69 2GC0 PAN 4.25532
70 3WW2 SF6 4.29688
71 3WW2 LPK 4.29688
72 5IXH OTP 4.34783
73 3E85 BSU 4.43038
74 3I7S PYR 4.45205
75 2VL1 GLY GLY 4.4586
76 1ZZ7 S0H 4.54545
77 6GW4 CHO 4.56026
78 4ZU4 4TG 4.72973
79 4XAC AKG 4.7619
80 5YBN AKG 4.77707
81 5C5T AKG 4.82456
82 3MPB FRU 4.87805
83 6B9R 2HE 4.88889
84 4YVN EBS 5.09554
85 2RDQ AKG 5.20833
86 5FPX GLY SER SER HIS HIS HIS HIS HIS 5.30973
87 2NNQ T4B 5.34351
88 3PUA OGA 5.35714
89 2I8T GDD 5.38922
90 5C3R AKG 5.53936
91 5C3R HMU 5.53936
92 5XEG AKG 5.62771
93 6F4T OGA 5.88235
94 1OIK AKG 5.98007
95 1OIJ AKG 5.98007
96 1OIK C26 5.98007
97 5YGF ASP GLN GLY ARG GLY ARG ARG ARG PRO 6.27803
98 5FLJ QUE 6.45161
99 3R6K FUC GAL GLA 6.55738
100 2MPR BGC GLC GLC 6.55738
101 2CM4 RCL 6.66667
102 3ACL 3F1 6.75676
103 1LSH PLD 6.89655
104 1GP6 QUE 7.02247
105 1GP6 SIN 7.02247
106 1GP6 DH2 7.02247
107 4QXB OGA 7.35294
108 2FB3 GTP 7.35294
109 5O9W AKG 7.35695
110 1VKF CIT 7.44681
111 4Q0P 0MK 7.69231
112 2A1X AKG 7.79221
113 4J25 OGA 7.86026
114 2JIG PD2 8.03571
115 5EPA AKG 8.24373
116 6B9T 2HE 8.3151
117 1DRY AAG 8.33333
118 1DRY AKG 8.33333
119 2ET1 GLV 8.95522
120 5I0U DCY 9
121 6FXR AKG 9.12951
122 4XCB HY0 9.1954
123 4XCB AKG 9.1954
124 5NIU 8YZ 9.375
125 5N2F 8HW 10.4839
126 5N2D 8J8 11.1111
127 6GNO XDI 13.3333
128 4QM9 CYS 13.8728
129 1LRH NLA 14.7239
130 4F7E 0SH 16.3265
131 4CCN OGA 17.1429
132 5WL1 D3D 23.2323
133 5WL1 CUY 23.2323
134 4CCO OGA 35
135 3OPT AKG 42.0912
136 2YBP 2HG 42.2572
137 2OS2 OGA 42.2572
138 5F3I 5UJ 44.7222
139 2XUM OGA 50
Pocket No.: 2; Query (leader) PDB : 5FWJ; Ligand: MMK; Similar sites found with APoc: 9
This union binding pocket(no: 2) in the query (biounit: 5fwj.bio2) has 15 residues
No: Leader PDB Ligand Sequence Similarity
1 5FYR INS 1.67785
2 2RKV ZBA 1.99557
3 2XCG XCG 2.33546
4 5FSY AR6 3.00752
5 2WSA 646 3.39703
6 2WSA MYA 3.39703
7 4WN5 MVC 5.21739
8 3HCH RSM 6.84932
9 6D6L FY4 10
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