Receptor
PDB id Resolution Class Description Source Keywords
5A3T 1.9 Å EC: 1.14.11.- CRYSTAL STRUCTURE OF HUMAN PLU-1 (JARID1B) IN COMPLEX WITH KDM5-C49 (2-(((2-((2-(DIMETHYLAMINO)ETHYL)(ETHYL)AMINO)-2- O XOETHYL)AMINO)METHYL) ISONICOTINIC ACID). HOMO SAPIENS OXIDOREDUCTASE LYSINE-SPECIFIC DEMETHYLASE 5B
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
ZN A:1754;
Invalid;
none;
submit data
65.409 Zn [Zn+2...
EDO A:1760;
A:1763;
A:1762;
A:1758;
A:1764;
A:1761;
A:1759;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
none;
none;
none;
none;
none;
none;
none;
submit data
62.068 C2 H6 O2 C(CO)...
MMK A:1756;
Valid;
none;
Ki = 0.001 uM
306.36 C15 H22 N4 O3 CCN(/...
MN A:1765;
Invalid;
none;
submit data
54.938 Mn [Mn+2...
NI A:1757;
Invalid;
none;
submit data
58.693 Ni [Ni+2...
EPE A:1755;
Invalid;
none;
submit data
238.305 C8 H18 N2 O4 S C1CN(...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
5A3T 1.9 Å EC: 1.14.11.- CRYSTAL STRUCTURE OF HUMAN PLU-1 (JARID1B) IN COMPLEX WITH KDM5-C49 (2-(((2-((2-(DIMETHYLAMINO)ETHYL)(ETHYL)AMINO)-2- O XOETHYL)AMINO)METHYL) ISONICOTINIC ACID). HOMO SAPIENS OXIDOREDUCTASE LYSINE-SPECIFIC DEMETHYLASE 5B
Ref.: STRUCTURAL ANALYSIS OF HUMAN KDM5B GUIDES HISTONE DEMETHYLASE INHIBITOR DEVELOPMENT. NAT.CHEM.BIOL. V. 12 539 2016
Members (9)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 26 families.
1 5A3N ic50 = 19 nM LQT C15 H25 N5 O2 CCN(CCN(C)....
2 5A3W Ki = 0.39 uM PD2 C7 H5 N O4 c1cnc(cc1C....
3 5FPL - MN QAY n/a n/a
4 5FPU Ki = 0.14 uM K0I C22 H23 N5 O2 c1ccc2c(c1....
5 5FUP - AKG C5 H6 O5 C(CC(=O)O)....
6 5FV3 Ki = 6.32 uM OGA C4 H5 N O5 C(C(=O)O)N....
7 5A1F Ki = 6.32 uM OGA C4 H5 N O5 C(C(=O)O)N....
8 5FUN Ki = 0.01 uM GZA C17 H13 N5 O2 c1ccc(cc1)....
9 5A3T Ki = 0.001 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 18 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 (23)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 17 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 5IVY Kd = 0.36 uM 6EO C14 H11 Cl N2 O3 c1cc(ccc1C....
4 5IWF - LQT C15 H25 N5 O2 CCN(CCN(C)....
5 5IVC Kd = 1.2 uM 6E7 C20 H17 N3 O3 c1ccc(cc1)....
6 5IVV Kd = 0.45 uM 6EN C14 H12 N4 O2 Cn1cc(c2c1....
7 5ISL Kd = 0.052 uM MMK C15 H22 N4 O3 CCN(/C=C/N....
8 5E6H Kd = 79 uM AKG C5 H6 O5 C(CC(=O)O)....
9 5IW0 Kd = 0.06 uM 6EP C17 H14 Cl N3 O3 Cc1cc(ccc1....
10 5IVJ Kd = 0.046 uM 6ED C20 H20 F3 N5 O2 c1cc2c(cc1....
11 5IVB - AKG C5 H6 O5 C(CC(=O)O)....
12 5IVF - 6EB C15 H14 F3 N5 O2 Cn1cc(nc1)....
13 5A3N ic50 = 19 nM LQT C15 H25 N5 O2 CCN(CCN(C)....
14 5A3W Ki = 0.39 uM PD2 C7 H5 N O4 c1cnc(cc1C....
15 5FPL - MN QAY n/a n/a
16 5FPU Ki = 0.14 uM K0I C22 H23 N5 O2 c1ccc2c(c1....
17 5FUP - AKG C5 H6 O5 C(CC(=O)O)....
18 5FV3 Ki = 6.32 uM OGA C4 H5 N O5 C(C(=O)O)N....
19 5A1F Ki = 6.32 uM OGA C4 H5 N O5 C(C(=O)O)N....
20 5FUN Ki = 0.01 uM GZA C17 H13 N5 O2 c1ccc(cc1)....
21 5A3T Ki = 0.001 uM MMK C15 H22 N4 O3 CCN(/C=C/N....
22 4IGQ - OGA C4 H5 N O5 C(C(=O)O)N....
23 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 : 5A3T; Ligand: MMK; Similar sites found: 181
This union binding pocket(no: 1) in the query (biounit: 5a3t.bio1) has 32 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 5VE5 GSH 0.03381 0.40677 1.06101
2 4FFG 0U8 0.006558 0.44592 1.2474
3 3JQ3 ADP 0.0007094 0.48517 1.36612
4 4YRD 3IT 0.001161 0.47998 1.39276
5 4D4U FUC NDG GAL FUC 0.005631 0.44706 1.5873
6 2X05 X05 0.02513 0.40317 1.6632
7 3ACL 3F1 0.001959 0.44893 1.68919
8 4K3H 1OM 0.002813 0.43005 1.69492
9 3PUA OGA 0.0002601 0.52199 1.78571
10 1O68 KIV 0.02975 0.41084 1.81818
11 3URB DPF 0.03796 0.40562 1.83486
12 3ZDS HQ9 0.001798 0.47678 1.84758
13 3ZDS HMQ 0.001779 0.46503 1.84758
14 3ZDS OMD 0.003003 0.45858 1.84758
15 3ZDS M8O 0.003876 0.45284 1.84758
16 5KJW 53C 0.03538 0.40473 1.87354
17 4XCB AKG 0.001399 0.48155 1.91571
18 4XCB HY0 0.004682 0.40507 1.91571
19 5LUN OGA 0.00229 0.47019 1.98864
20 5LUN ARG 0.03881 0.40075 1.98864
21 3MPB FRU 0.01903 0.40562 2.03252
22 1ZM1 BGC BGC BGC 0.01387 0.40878 2.07469
23 3KV5 OGA 0.00104 0.48309 2.079
24 4J25 OGA 0.0006191 0.50293 2.18341
25 3KV4 OGA 0.004422 0.45494 2.23714
26 3PQB VGP 0.006462 0.41085 2.2869
27 4Y3O OGA 0.00002382 0.57948 2.36052
28 3JU6 ANP 0.0009289 0.49097 2.43243
29 2OVW CBI 0.001081 0.48151 2.43309
30 1DZK PRZ 0.02123 0.4 2.54777
31 4YVN EBS 0.00254 0.47138 2.7027
32 3WG3 A2G GAL NAG FUC 0.04605 0.40104 2.80899
33 4GC1 MAN MAN 0.008487 0.41879 2.89855
34 1OIJ AKG 0.01579 0.41539 2.99003
35 2HKA C3S 0.004484 0.42453 3.07692
36 1GP6 DH2 0.001284 0.43095 3.08989
37 1GP6 SIN 0.001284 0.43095 3.08989
38 1GP6 QUE 0.001357 0.42677 3.08989
39 3BP1 GUN 0.02007 0.41167 3.10345
40 3HX3 RET 0.01094 0.41024 3.16456
41 4NZ6 DLY 0.01133 0.43384 3.19489
42 2YKL NLD 0.02361 0.40452 3.24074
43 2WZ5 MET 0.001866 0.4492 3.26797
44 3K3K A8S 0.009685 0.40622 3.31754
45 3FW9 SLX 0.006357 0.41766 3.3264
46 4BG4 ADP 0.0107 0.41069 3.37079
47 3NBC LAT 0.03429 0.4072 3.37838
48 3A76 SPD 0.008553 0.44048 3.40909
49 4IMO PWZ 0.01348 0.43083 3.40909
50 3HCH RSM 0.04608 0.40074 3.42466
51 4RKX 3S9 0.03189 0.40922 3.44828
52 4ZXA H8N 0.0008129 0.48792 3.57143
53 4POS NAG SIA GAL 0.01625 0.41644 3.59712
54 5UQD AKG 0.00003178 0.57367 3.61991
55 4MJ0 BGC SIA SIA GAL 0.0389 0.40402 3.63636
56 2Z93 END 0.01725 0.4077 3.66972
57 4IAW LIZ 0.004181 0.44629 3.7234
58 1SR9 KIV 0.03203 0.41056 3.7422
59 5V1B 8UY 0.01424 0.42798 3.75
60 1O4T OXL 0.01829 0.41179 3.7594
61 1NJJ GET 0.02436 0.41533 3.76471
62 5C3R HMU 0.0002203 0.48853 3.79009
63 5C3R AKG 0.0002203 0.48853 3.79009
64 2Z48 NGA 0.0132 0.41162 3.93519
65 2Z48 A2G 0.02427 0.4108 3.93519
66 4EE7 PIS 0.02016 0.42254 3.94737
67 3KYG 5GP 5GP 0.01519 0.40691 3.96476
68 5AIG VPR 0.02489 0.41087 4
69 4LH7 1X8 0.00972 0.442 4.02477
70 2ZL7 FUC GAL NGA 0.04917 0.40093 4.0678
71 3P3Z P3Z 0.04223 0.40235 4.08654
72 3W68 4PT 0.009968 0.43579 4.13534
73 3U6W KIV 0.0372 0.40711 4.21546
74 4GQP B40 0.01154 0.43413 4.41767
75 1SDW IYT 0.01791 0.41048 4.4586
76 1A78 TDG 0.02079 0.4064 4.47761
77 5NBW 8SK 0.01278 0.41776 4.5045
78 3PB9 1BN 0.023 0.40876 4.54545
79 4YLZ LAT NAG GAL 0.008732 0.44205 4.57516
80 1OGX EQU 0.01479 0.41094 4.58015
81 2J5B TYE 0.009025 0.4411 4.5977
82 2G30 ALA ALA PHE 0.001494 0.50255 4.65116
83 4XAC AKG 0.01065 0.43449 4.7619
84 4WCX MET 0.01856 0.42133 4.79167
85 1EPB REA 0.00454 0.43172 4.87805
86 3SAO NKN 0.007348 0.43391 5
87 5BWD FUM 0.04349 0.40233 5
88 5EPA AKG 0.007217 0.44371 5.01792
89 5I8T LAC 0.03622 0.40624 5.02793
90 4H6B 10Y 0.01674 0.41987 5.12821
91 4WN5 MVC 0.006695 0.40716 5.21739
92 1J3R 6PG 0.000102 0.52765 5.26316
93 2GC0 PAN 0.0004117 0.47601 5.31915
94 5FLJ QUE 0.009542 0.40348 5.37634
95 5IQT AKG 0.001051 0.44898 5.39683
96 5IQT 6CU 0.0007392 0.4443 5.39683
97 2RDQ AKG 0.0001984 0.47657 5.55556
98 5K21 6QF 0.03131 0.40191 5.67376
99 1QH5 GBP 0.02382 0.41596 5.76923
100 5T7I LAT NAG GAL 0.00187 0.47853 5.80645
101 4RYV ZEA 0.009759 0.42768 5.80645
102 5X7Q GLC GLC GLC GLC GLC 0.00828 0.44112 5.82121
103 5X7Q GLC GLC 0.01511 0.41557 5.82121
104 4FE2 AIR 0.01494 0.4183 5.88235
105 1H8S AIC 0.006962 0.43966 5.95238
106 3NX2 FER 0.01033 0.42726 5.95238
107 4GJY OGA 0.000001276 0.6502 5.95745
108 5FUI APY 0.003126 0.46289 6.06061
109 5HZX 2GE 0.02743 0.40485 6.25
110 4CC6 L5Y 0.03061 0.40617 6.28931
111 2HRL SIA GAL SIA BGC NGA CEQ 0.03582 0.40258 6.29921
112 3ML5 AZM 0.04469 0.40321 6.3197
113 2GQS C2R 0.01966 0.40493 6.32911
114 3H7J PPY 0.007965 0.42395 6.58436
115 3B00 16A 0.01948 0.41243 6.61765
116 3T4L ZEA 0.004654 0.42741 6.66667
117 4ZU4 4TG 0.004836 0.43042 6.75676
118 5KEW 6SB 0.038 0.40511 6.94444
119 2YG2 S1P 0.005628 0.41038 6.97674
120 3PUR 2HG 0.002546 0.46955 7.06861
121 3N9O OGA 0.003542 0.45948 7.06861
122 3N9Q OGA 0.004115 0.45486 7.06861
123 3N9P OGA 0.004833 0.45129 7.06861
124 2G50 PYR 0.022 0.41858 7.06861
125 4KYS VIB 0.04129 0.40316 7.06861
126 5FPX GLY SER SER HIS HIS HIS HIS HIS 0.000125 0.49478 7.07965
127 5NCF 8T5 0.007214 0.44372 7.07965
128 5L9V OGA 0.007989 0.43208 7.14286
129 5L9B AKG 0.01277 0.42175 7.14286
130 1M3U KPL 0.02354 0.41214 7.19697
131 4JH6 FCN 0.03676 0.40199 7.24638
132 3P7N FMN 0.01188 0.40534 7.36434
133 4JGP PYR 0.0314 0.41058 7.37327
134 1GT4 UNA 0.01398 0.40862 7.54717
135 5F90 GLA GAL 0.04477 0.41071 7.69231
136 2ZQO NGA 0.04668 0.40045 7.69231
137 5C5T AKG 0.001335 0.47679 7.89474
138 2ARC ARA 0.01133 0.42869 7.92683
139 4UCI ADN 0.007032 0.4581 7.95181
140 3W21 AKG 0.01344 0.41609 8.05861
141 1OS7 AKG 0.001578 0.44116 8.12721
142 1OS7 TAU 0.001578 0.44116 8.12721
143 4GLW 0XT 0.03077 0.40604 8.19672
144 4WVO 3UZ 0.004415 0.40339 8.28729
145 5JSP DQY 0.001335 0.48397 8.45771
146 2JIG PD2 0.0002178 0.51748 8.48214
147 4N14 WR7 0.0159 0.43307 8.59873
148 1EX7 5GP 0.03082 0.41002 8.60215
149 1TUV VK3 0.03866 0.41976 8.77193
150 2AGC DAO 0.01754 0.41881 9.25926
151 2ZHL NAG GAL GAL NAG 0.02066 0.40741 9.45946
152 4K55 H6P 0.01453 0.41735 9.67742
153 2QL9 CIT 0.002349 0.47223 9.82659
154 1DTD GLU 0.03434 0.40622 9.83607
155 5TFZ 7BC 0.0004535 0.50102 10
156 4DSU BZI 0.008687 0.4468 10.0529
157 3W9R A8S 0.01145 0.42012 10.0529
158 5XLY C2E 0.005575 0.42379 10.5263
159 2XOM GAL GAL GAL 0.03291 0.40656 10.5263
160 3NMV PYV 0.01241 0.41107 10.6742
161 2FCU AKG 0.003379 0.46252 10.8626
162 5H9P TD2 0.01249 0.43103 12.0253
163 4QM9 CYS 0.004088 0.45702 13.2948
164 4NTX AMR 0.007481 0.40447 13.3333
165 1YQC GLV 0.01348 0.40379 13.5294
166 5E89 TD2 0.01992 0.40131 13.6691
167 4QXB OGA 0.000633 0.49353 14.7059
168 1LRH NLA 0.0006864 0.48589 14.7239
169 4HN1 TYD 0.005212 0.44146 14.9254
170 1N5S ADL 0.01014 0.41523 15.1786
171 2QX0 PH2 0.01888 0.42671 15.7233
172 1UYY BGC BGC 0.01869 0.42168 16.0305
173 3MYZ TFX 0.0003777 0.54439 17
174 1QY1 PRZ 0.007529 0.40796 20.1149
175 1SQL GUN 0.02407 0.41202 20.5479
176 5LDQ NAP 0.004411 0.45945 24.2938
177 4RT1 C2E 0.01219 0.41144 30.3571
178 3OPT AKG 0.000000003233 0.79008 42.0912
179 2OS2 OGA 0.0000000005216 0.83425 42.7822
180 2YBP 2HG 0.0000000009132 0.82064 42.7822
181 5F3I 5UJ 0.0000000003923 0.70347 45.2778
182 2XUM OGA 0.00002253 0.57857 50
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