Receptor
PDB id Resolution Class Description Source Keywords
6YVW 1.97 Å EC: 1.14.11.29 HIF PROLYL HYDROXYLASE 2 (PHD2/ EGLN1) IN COMPLEX WITH MONOC 328 HOMO SAPIENS OXIDOREDUCTASE NON-HEME DIOXYGENASE IRON 2-OXOGLUTARATE INDUCIBLE FACTOR HIF HIF PROLYL HYDROXYLASE DOMAIN 2 PHDOXYGENASE HYPOXIA DNA-BINDING METAL-BINDING TRANSCRIPTIHELIX-LOOP-HELIX-BETA DSBH FACIAL TRIAD CYTOPLASM TRANSCRIPTION/EPIGENETIC REGULATION SIGNALING DEVELOPMENTSTRUCTURE BETA-HYDROXYLATION TRANSCRIPTION ACTIVATOR/INHIUBL CONJUGATION POLYMORPHISM VITAMIN C ZINC-FINGER FAMIERYTHROCYTOSIS BREAST CANCER TRANSCRIPTION COMPLEX
Ref.: USE OF CYCLIC PEPTIDES TO INDUCE CRYSTALLIZATION: C WITH PROLYL HYDROXYLASE DOMAIN 2. SCI REP V. 10 21964 2020
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
GOL A:503;
 Invalid;
 none;
 submit data
92.094 C3 H8 O3 C(C(C...
FE A:501;
 Part of Protein;
 none;
 submit data
55.845 Fe [Fe+3...
PW5 A:502;
 Valid;
 none;
 submit data
301.137 C11 H13 Br N2 O3 Cc1cc...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
6NMQ 1.58 Å EC: 1.14.11.29 HYPOXIA-INDUCIBLE FACTOR (HIF) PROLYL HYDROXYLASE 2 (PHD2) I WITH THE CARBOXAMIDE ANALOG JNJ43058171 HOMO SAPIENS PHD2 HYPOXIA-INDUCIBLE FACTOR PROLYL HYDROXYLASE IRON-CONTENZYME CINNOLINE OXIDOREDUCTASE
Ref.: BEYOND TRADITIONAL STRUCTURE-BASED DRUG DESIGN: THE IRON COMPLEXATION, STRAIN, AND WATER IN THE BINDING INHIBITORS FOR HYPOXIA-INDUCIBLE FACTOR PROLYL HYDR 2. ACS OMEGA V. 4 6703 2019
Members (26)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 9 families.
1 6QGV ic50 = 0.127 uM J2H C30 H28 N6 O2 Cc1cccnc1C....
2 4JZR ic50 = 15.8 nM 4JR C25 H28 N4 O Cn1ccnc1CN....
3 4BQW - QNM C13 H12 N2 O5 CN1c2ccccc....
4 5LBC - UN9 C12 H9 Cl N2 O4 c1ccc2c(c1....
5 6NMQ ic50 = 0.00000001 M KU1 C11 H9 N3 O4 c1ccc2c(c1....
6 4BQX - UN9 C12 H9 Cl N2 O4 c1ccc2c(c1....
7 2Y34 - UN9 C12 H9 Cl N2 O4 c1ccc2c(c1....
8 5L9R - OGA C4 H5 N O5 C(C(=O)O)N....
9 5LBF - UN9 C12 H9 Cl N2 O4 c1ccc2c(c1....
10 6YW0 - 2JP C13 H12 N2 O3 c1ccc2cnc(....
11 4BQY - FNT C13 H11 Cl N2 O4 C[C@@H](C(....
12 5OX5 ic50 = 2.6 uM B2E C9 H11 N3 O6 CN1C(=C(C(....
13 5OX6 ic50 = 0.029 uM A1Z C14 H11 Cl N2 O4 c1cc(cc(c1....
14 6YVZ - PW8 C13 H11 Br N2 O3 c1cc2cnc(c....
15 5LAT - UN9 C12 H9 Cl N2 O4 c1ccc2c(c1....
16 5V18 - 8UY C13 H8 N4 c1cc(n2c(c....
17 6YVW - PW5 C11 H13 Br N2 O3 Cc1cc(nc(c....
18 2G1M - 4HG C12 H9 I N2 O4 c1cc2c(cnc....
19 6ST3 ic50 = 0.256 uM LUW C21 H17 N5 O3 c1ccc(cc1)....
20 2Y33 - UN9 C12 H9 Cl N2 O4 c1ccc2c(c1....
21 5LB6 - UN9 C12 H9 Cl N2 O4 c1ccc2c(c1....
22 6YVX - 2JP C13 H12 N2 O3 c1ccc2cnc(....
23 2G19 - 4HG C12 H9 I N2 O4 c1cc2c(cnc....
24 5LBE - UN9 C12 H9 Cl N2 O4 c1ccc2c(c1....
25 4UWD - UN9 C12 H9 Cl N2 O4 c1ccc2c(c1....
26 5LBB - UN9 C12 H9 Cl N2 O4 c1ccc2c(c1....
70% Homology Family (27)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 6 families.
1 6QGV ic50 = 0.127 uM J2H C30 H28 N6 O2 Cc1cccnc1C....
2 4JZR ic50 = 15.8 nM 4JR C25 H28 N4 O Cn1ccnc1CN....
3 4BQW - QNM C13 H12 N2 O5 CN1c2ccccc....
4 5LBC - UN9 C12 H9 Cl N2 O4 c1ccc2c(c1....
5 6NMQ ic50 = 0.00000001 M KU1 C11 H9 N3 O4 c1ccc2c(c1....
6 4BQX - UN9 C12 H9 Cl N2 O4 c1ccc2c(c1....
7 2Y34 - UN9 C12 H9 Cl N2 O4 c1ccc2c(c1....
8 5L9R - OGA C4 H5 N O5 C(C(=O)O)N....
9 5LBF - UN9 C12 H9 Cl N2 O4 c1ccc2c(c1....
10 6YW0 - 2JP C13 H12 N2 O3 c1ccc2cnc(....
11 4BQY - FNT C13 H11 Cl N2 O4 C[C@@H](C(....
12 5OX5 ic50 = 2.6 uM B2E C9 H11 N3 O6 CN1C(=C(C(....
13 5OX6 ic50 = 0.029 uM A1Z C14 H11 Cl N2 O4 c1cc(cc(c1....
14 6YVZ - PW8 C13 H11 Br N2 O3 c1cc2cnc(c....
15 5LAT - UN9 C12 H9 Cl N2 O4 c1ccc2c(c1....
16 5V18 - 8UY C13 H8 N4 c1cc(n2c(c....
17 6YVW - PW5 C11 H13 Br N2 O3 Cc1cc(nc(c....
18 2G1M - 4HG C12 H9 I N2 O4 c1cc2c(cnc....
19 6ST3 ic50 = 0.256 uM LUW C21 H17 N5 O3 c1ccc(cc1)....
20 2Y33 - UN9 C12 H9 Cl N2 O4 c1ccc2c(c1....
21 5LB6 - UN9 C12 H9 Cl N2 O4 c1ccc2c(c1....
22 6YVX - 2JP C13 H12 N2 O3 c1ccc2cnc(....
23 2G19 - 4HG C12 H9 I N2 O4 c1cc2c(cnc....
24 5LBE - UN9 C12 H9 Cl N2 O4 c1ccc2c(c1....
25 4UWD - UN9 C12 H9 Cl N2 O4 c1ccc2c(c1....
26 5LBB - UN9 C12 H9 Cl N2 O4 c1ccc2c(c1....
27 5V1B ic50 = 0.034 uM 8UY C13 H8 N4 c1cc(n2c(c....
50% Homology Family (27)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 6 families.
1 6QGV ic50 = 0.127 uM J2H C30 H28 N6 O2 Cc1cccnc1C....
2 4JZR ic50 = 15.8 nM 4JR C25 H28 N4 O Cn1ccnc1CN....
3 4BQW - QNM C13 H12 N2 O5 CN1c2ccccc....
4 5LBC - UN9 C12 H9 Cl N2 O4 c1ccc2c(c1....
5 6NMQ ic50 = 0.00000001 M KU1 C11 H9 N3 O4 c1ccc2c(c1....
6 4BQX - UN9 C12 H9 Cl N2 O4 c1ccc2c(c1....
7 2Y34 - UN9 C12 H9 Cl N2 O4 c1ccc2c(c1....
8 5L9R - OGA C4 H5 N O5 C(C(=O)O)N....
9 5LBF - UN9 C12 H9 Cl N2 O4 c1ccc2c(c1....
10 6YW0 - 2JP C13 H12 N2 O3 c1ccc2cnc(....
11 4BQY - FNT C13 H11 Cl N2 O4 C[C@@H](C(....
12 5OX5 ic50 = 2.6 uM B2E C9 H11 N3 O6 CN1C(=C(C(....
13 5OX6 ic50 = 0.029 uM A1Z C14 H11 Cl N2 O4 c1cc(cc(c1....
14 6YVZ - PW8 C13 H11 Br N2 O3 c1cc2cnc(c....
15 5LAT - UN9 C12 H9 Cl N2 O4 c1ccc2c(c1....
16 5V18 - 8UY C13 H8 N4 c1cc(n2c(c....
17 6YVW - PW5 C11 H13 Br N2 O3 Cc1cc(nc(c....
18 2G1M - 4HG C12 H9 I N2 O4 c1cc2c(cnc....
19 6ST3 ic50 = 0.256 uM LUW C21 H17 N5 O3 c1ccc(cc1)....
20 2Y33 - UN9 C12 H9 Cl N2 O4 c1ccc2c(c1....
21 5LB6 - UN9 C12 H9 Cl N2 O4 c1ccc2c(c1....
22 6YVX - 2JP C13 H12 N2 O3 c1ccc2cnc(....
23 2G19 - 4HG C12 H9 I N2 O4 c1cc2c(cnc....
24 5LBE - UN9 C12 H9 Cl N2 O4 c1ccc2c(c1....
25 4UWD - UN9 C12 H9 Cl N2 O4 c1ccc2c(c1....
26 5LBB - UN9 C12 H9 Cl N2 O4 c1ccc2c(c1....
27 5V1B ic50 = 0.034 uM 8UY C13 H8 N4 c1cc(n2c(c....
Polypharmacology
Similar Ligands (2D)
Ligand no: 1; Ligand: PW5; Similar ligands found: 2
No: Ligand ECFP6 Tc MDL keys Tc
1 PW5 1 1
2 SX2 0.448276 0.893617
Similar Ligands (3D)
Ligand no: 1; Ligand: PW5; Similar ligands found: 91
No: Ligand Similarity coefficient
1 5TU 0.9336
2 STL 0.9090
3 3N0 0.9087
4 WG8 0.9069
5 G30 0.9069
6 IW3 0.9052
7 LJ5 0.9050
8 1Q1 0.9045
9 PW8 0.9042
10 KWV 0.9022
11 68C 0.9008
12 2JP 0.9001
13 ZEA 0.8988
14 1Q2 0.8984
15 3K1 0.8932
16 LJ2 0.8932
17 IJ4 0.8927
18 D26 0.8918
19 GJW 0.8911
20 FBC 0.8898
21 PIT 0.8897
22 GOE 0.8886
23 XAV 0.8879
24 D25 0.8879
25 7KE 0.8868
26 8GP 0.8867
27 C9M 0.8867
28 IW5 0.8859
29 UN9 0.8840
30 4ZF 0.8839
31 801 0.8835
32 8M5 0.8833
33 IJ1 0.8820
34 3D3 0.8820
35 RKY 0.8815
36 0V7 0.8811
37 0K7 0.8794
38 2OX 0.8789
39 JZR 0.8787
40 27F 0.8787
41 L02 0.8781
42 83D 0.8780
43 SNV 0.8770
44 5HG 0.8767
45 7FZ 0.8762
46 5ER 0.8761
47 RE4 0.8757
48 BXS 0.8751
49 0RY 0.8741
50 IGP 0.8737
51 8CC 0.8736
52 Q5M 0.8732
53 C0V 0.8730
54 7HV 0.8721
55 KHP 0.8720
56 D2G 0.8717
57 FNT 0.8713
58 35K 0.8713
59 M01 0.8711
60 1BW 0.8710
61 JKK 0.8695
62 EMU 0.8691
63 27K 0.8685
64 CWL 0.8684
65 UN4 0.8682
66 KU1 0.8678
67 OAK 0.8678
68 SNP 0.8675
69 7GP 0.8675
70 L15 0.8674
71 WA2 0.8672
72 L2K 0.8669
73 OQR 0.8665
74 RE2 0.8655
75 NZ4 0.8655
76 P1J 0.8654
77 IW4 0.8649
78 5QT 0.8648
79 N9M 0.8643
80 2KU 0.8632
81 S8G 0.8626
82 GVI 0.8618
83 245 0.8616
84 CMG 0.8616
85 JCL 0.8614
86 S45 0.8613
87 FHV 0.8576
88 KLS 0.8568
89 3NB 0.8550
90 KWK 0.8549
91 SIJ 0.8522
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 6NMQ; Ligand: KU1; Similar sites found with APoc: 5
This union binding pocket(no: 1) in the query (biounit: 6nmq.bio1) has 28 residues
No: Leader PDB Ligand Sequence Similarity
1 6KUN AKG 4.69484
2 6KUN AKG 4.69484
3 6TTN OGA 5.6338
4 4J25 OGA 38.9671
5 4J25 OGA 38.9671
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