Receptor
PDB id Resolution Class Description Source Keywords
6AVS 2.02 Å EC: 1.14.11.27 COMPLEX STRUCTURE OF JMJD5 AND SYMMETRIC MONOMETHYL-ARGININE HOMO SAPIENS DEMETHYLASE JUMONJI HISTONE ENDOPEPTIDASE EXOPEPTIDASE OXIDOREDUCTASE
Ref.: SPECIFIC RECOGNITION OF ARGININE METHYLATED HISTONE JMJD5 AND JMJD7. SCI REP V. 8 3275 2018
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
NMM A:502;
 Valid;
 none;
 submit data
188.228 C7 H16 N4 O2 [H]/N...
ZN A:501;
 Part of Protein;
 none;
 submit data
65.409 Zn [Zn+2...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
6F4T 1.22 Å EC: 1.14.11.27 HUMAN JMJD5 (W414C) IN COMPLEX WITH MN(II), NOG AND RCCD1 (1 (COMPLEX-5) HOMO SAPIENS OXIDOREDUCTASE NON-HEME IRON 2-OXOGLUTARATE DIOXYGENASEJMJC DOMAIN LYSINE-SPECIFIC DEMETHYLASE 8 JMJC DOMAIN-CONPROTEIN 5 ARGINYL C-3 HYDROXYLASE JMJD5 KDM8 OXYGENASEDNA-BINDING METAL-BINDING TRANSLATION DSBH FACIAL TRIADCYTOPLASM JMJC HYDROXYLASE JMJC DEMETHYLASE KDMS POST- TRANSLATIONAL MODIFICATIONS PTM BETA-HYDROXYLATION HYDROARGININE HYDROXYLATION RCC1 DOMAIN-CONTAINING PROTEIN 1 RREGULATOR OF CHROMOSOME CONDENSATION 40S RIBOSOMAL PROTEINRPS6 RIBOSOME BIOGENESIS TRANSCRIPTION EPIGENETIC REGULASIGNALING DEVELOPMENT CELL STRUCTURE TRANSCRIPTION ACTIVATOR/INHIBITOR PHOSPHORYLATION CANCER POLYMORPHISM
Ref.: JMJD5 IS A HUMAN ARGINYL C-3 HYDROXYLASE. NAT COMMUN V. 9 1180 2018
Members (11)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 7 families.
1 6AX3 - 2MR C8 H18 N4 O2 CN/C(=N/C)....
2 6AVS - NMM C7 H16 N4 O2 [H]/N=C(/N....
3 6I9L - PD2 C7 H5 N O4 c1cnc(cc1C....
4 6F4O - SIN C4 H6 O4 C(CC(=O)O)....
5 4GJY - OGA C4 H5 N O5 C(C(=O)O)N....
6 6I9M - 2HG C5 H8 O5 C(CC(=O)O)....
7 6F4R ic50 = 6 uM OGA C4 H5 N O5 C(C(=O)O)N....
8 6F4S - AKG C5 H6 O5 C(CC(=O)O)....
9 4GJZ - AKG C5 H6 O5 C(CC(=O)O)....
10 6I9N - S2G C5 H8 O5 C(CC(=O)O)....
11 6F4T ic50 = 6 uM OGA C4 H5 N O5 C(C(=O)O)N....
70% Homology Family (11)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 6 families.
1 6AX3 - 2MR C8 H18 N4 O2 CN/C(=N/C)....
2 6AVS - NMM C7 H16 N4 O2 [H]/N=C(/N....
3 6I9L - PD2 C7 H5 N O4 c1cnc(cc1C....
4 6F4O - SIN C4 H6 O4 C(CC(=O)O)....
5 4GJY - OGA C4 H5 N O5 C(C(=O)O)N....
6 6I9M - 2HG C5 H8 O5 C(CC(=O)O)....
7 6F4R ic50 = 6 uM OGA C4 H5 N O5 C(C(=O)O)N....
8 6F4S - AKG C5 H6 O5 C(CC(=O)O)....
9 4GJZ - AKG C5 H6 O5 C(CC(=O)O)....
10 6I9N - S2G C5 H8 O5 C(CC(=O)O)....
11 6F4T ic50 = 6 uM OGA C4 H5 N O5 C(C(=O)O)N....
50% Homology Family (11)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 5 families.
1 6AX3 - 2MR C8 H18 N4 O2 CN/C(=N/C)....
2 6AVS - NMM C7 H16 N4 O2 [H]/N=C(/N....
3 6I9L - PD2 C7 H5 N O4 c1cnc(cc1C....
4 6F4O - SIN C4 H6 O4 C(CC(=O)O)....
5 4GJY - OGA C4 H5 N O5 C(C(=O)O)N....
6 6I9M - 2HG C5 H8 O5 C(CC(=O)O)....
7 6F4R ic50 = 6 uM OGA C4 H5 N O5 C(C(=O)O)N....
8 6F4S - AKG C5 H6 O5 C(CC(=O)O)....
9 4GJZ - AKG C5 H6 O5 C(CC(=O)O)....
10 6I9N - S2G C5 H8 O5 C(CC(=O)O)....
11 6F4T ic50 = 6 uM OGA C4 H5 N O5 C(C(=O)O)N....
Polypharmacology
Similar Ligands (2D)
Ligand no: 1; Ligand: NMM; Similar ligands found: 38
No: Ligand ECFP6 Tc MDL keys Tc
1 NMM 1 1
2 HAR 0.707317 0.744186
3 1KJ 0.681818 0.790698
4 ILO 0.658537 0.837838
5 RPI 0.630435 0.615385
6 2KJ 0.625 0.733333
7 D20 0.625 0.790698
8 DA2 0.6 0.833333
9 CIR 0.6 0.725
10 AS1 0.591837 0.761905
11 4JK 0.590909 0.75
12 VUR 0.590909 0.769231
13 3KJ 0.586957 0.76087
14 2MR 0.586957 0.972222
15 DAR 0.585366 0.888889
16 ARG 0.585366 0.888889
17 WT2 0.577778 0.763158
18 JM2 0.574468 0.780488
19 LN6 0.55102 0.731707
20 JM7 0.54 0.738095
21 3AR 0.531915 0.846154
22 VIO 0.520833 0.731707
23 HRG 0.511111 0.888889
24 JM4 0.509434 0.744186
25 JM8 0.509434 0.761905
26 JM6 0.509434 0.785714
27 JM5 0.5 0.761905
28 2YH 0.489796 0.619048
29 ALY 0.478261 0.642857
30 MLZ 0.477273 0.74359
31 NNH 0.466667 0.688889
32 ORN 0.414634 0.714286
33 MLY 0.413043 0.636364
34 I58 0.411765 0.731707
35 9YT 0.409091 0.604651
36 AHL 0.408163 0.612245
37 5KJ 0.403846 0.68
38 AAR 0.4 0.7
Similar Ligands (3D)
Ligand no: 1; Ligand: NMM; Similar ligands found: 144
No: Ligand Similarity coefficient
1 J9Y 0.9520
2 NPI 0.9470
3 EGV 0.9461
4 IAR 0.9365
5 NOT 0.9340
6 GGB 0.9334
7 API 0.9287
8 26P 0.9255
9 SB7 0.9252
10 M3L 0.9249
11 6HN 0.9226
12 EXY 0.9151
13 6FG 0.9145
14 KAP 0.9137
15 ZZU 0.9106
16 PML 0.9100
17 OCA 0.9086
18 DHH 0.9051
19 KPV 0.9035
20 GVA 0.9009
21 NRG 0.8988
22 KLS 0.8978
23 L06 0.8974
24 LPA 0.8972
25 2NP 0.8970
26 6HO 0.8960
27 HNK 0.8949
28 11X 0.8938
29 2OR 0.8937
30 FB6 0.8925
31 6C9 0.8923
32 1PS 0.8920
33 OJD 0.8898
34 XRX 0.8895
35 4KJ 0.8892
36 6C5 0.8892
37 Z70 0.8888
38 BZQ 0.8883
39 6C4 0.8881
40 LVD 0.8879
41 CXP 0.8864
42 M5E 0.8863
43 XOG 0.8863
44 M5P 0.8853
45 G3M 0.8848
46 2J3 0.8842
47 5TO 0.8822
48 XRS 0.8820
49 ENO 0.8820
50 JZA 0.8814
51 0L1 0.8808
52 HL6 0.8807
53 M6H 0.8798
54 RGP 0.8794
55 9OD 0.8792
56 4ZD 0.8792
57 C82 0.8790
58 UN1 0.8786
59 8AC 0.8786
60 1VK 0.8775
61 6MW 0.8764
62 DZA 0.8764
63 2JJ 0.8758
64 DHM 0.8754
65 1HS 0.8753
66 11C 0.8753
67 TZM 0.8747
68 5PV 0.8740
69 CPZ 0.8740
70 O45 0.8739
71 JX7 0.8739
72 N8C 0.8739
73 SB9 0.8736
74 NCT 0.8736
75 F98 0.8732
76 IJ6 0.8729
77 SOJ 0.8728
78 SZ7 0.8726
79 PBN 0.8725
80 PAO 0.8724
81 I2E 0.8723
82 MSR 0.8722
83 AHN 0.8722
84 TZP 0.8720
85 PPY 0.8718
86 NBB 0.8707
87 2FM 0.8705
88 BNL 0.8705
89 EN1 0.8703
90 LPB 0.8698
91 PHQ DAL 0.8694
92 KDG 0.8692
93 PFF 0.8692
94 TYR 0.8691
95 3IP 0.8689
96 3VW 0.8683
97 FHC 0.8681
98 3GC 0.8678
99 492 0.8673
100 ODI 0.8671
101 9B3 0.8671
102 PHE 0.8670
103 D53 0.8669
104 3GZ 0.8668
105 19N 0.8665
106 PPT 0.8662
107 LYS 0.8661
108 4YZ 0.8658
109 4TP 0.8655
110 A5P 0.8652
111 SAF 0.8650
112 MF3 0.8649
113 54X 0.8644
114 JF5 0.8641
115 PA5 0.8639
116 22F 0.8638
117 TRP 0.8633
118 0OY 0.8631
119 HIC 0.8627
120 M4E 0.8624
121 N9J 0.8621
122 2UB 0.8620
123 LUQ 0.8614
124 4BX 0.8614
125 FXY 0.8613
126 4HP 0.8610
127 3YP 0.8599
128 D2G 0.8598
129 R10 0.8598
130 C53 0.8591
131 HHH 0.8590
132 SNU 0.8582
133 CH9 0.8579
134 RE4 0.8576
135 S7D 0.8573
136 D10 0.8568
137 1BN 0.8559
138 CK2 0.8555
139 EYV 0.8550
140 KYN 0.8545
141 SQ7 0.8533
142 7ZL 0.8530
143 YE6 0.8528
144 6FR 0.8527
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 6F4T; Ligand: OGA; Similar sites found with APoc: 5
This union binding pocket(no: 1) in the query (biounit: 6f4t.bio1) has 20 residues
No: Leader PDB Ligand Sequence Similarity
1 6GDY AKG 39.6078
2 2XUM OGA 46.2745
3 3P3N AKG 46.2745
4 2Y0I AKG 46.2745
5 4B7E OGA 46.2745
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