Receptor
PDB id Resolution Class Description Source Keywords
6RA1 2 Å EC: 5.2.1.8 HUMAN CYCLOPHILIN D IN COMPLEX WITH NORBORNANE FRAGMENT DERI HOMO SAPIENS CYCLOPHILIN BETA BARREL PROLYL CIS/TRANS ISOMERASE MITOCISOMERASE
Ref.: DISCOVERY OF NOVEL CYCLOPHILIN D INHIBITORS STARTIN THREE DIMENSIONAL FRAGMENTS WITH MILLIMOLAR POTENCI BIOORG.MED.CHEM.LETT. V. 29 26717 2019
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
PG4 A:304;
Invalid;
none;
submit data
194.226 C8 H18 O5 C(COC...
SO4 A:305;
A:306;
Invalid;
Invalid;
none;
none;
submit data
96.063 O4 S [O-]S...
JWB A:301;
Valid;
none;
submit data
223.225 C11 H13 N O4 C1C[C...
PEG A:303;
Invalid;
none;
submit data
106.12 C4 H10 O3 C(COC...
JVQ A:302;
Valid;
none;
submit data
248.278 C13 H16 N2 O3 CCN1C...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
6R8L 1.64 Å EC: 5.2.1.8 HUMAN CYCLOPHILIN D IN COMPLEX WITH 1-((1S,9S,10S)-10-HYDROX 8-AZA-TRICYCLO[7.3.1.02,7]TRIDECA-2,4,6-TRIEN-4-YLMETHYL)-32 -(2-METHYLSULFANYL-PHENYL)-PYRROLIDIN-1-YL]-2-OXO-ETHYL}-U HOMO SAPIENS CYCLOPHILIN BETA BARREL PROLYL CIS/TRANS ISOMERASE MITOCISOMERASE
Ref.: DISCOVERY OF NOVEL CYCLOPHILIN D INHIBITORS STARTIN THREE DIMENSIONAL FRAGMENTS WITH MILLIMOLAR POTENCI BIOORG.MED.CHEM.LETT. V. 29 26717 2019
Members (10)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 30 families.
1 6R9X Kd = 1.1 mM JW2 C13 H17 N3 O2 c1ccnc(c1)....
2 4ZSD - 7I6 C24 H32 N4 O2 S2 CSCC[C@@H]....
3 4XNC - EA4 C12 H17 N3 O3 CCOC(=O)CN....
4 4ZSC - EA4 C12 H17 N3 O3 CCOC(=O)CN....
5 6RA1 - JWB C11 H13 N O4 C1C[C@H]2C....
6 6R8W Kd = 1.2 uM JVH C23 H27 N3 O5 c1cc2c(cc1....
7 6R8O Kd = 0.67 uM JV2 C26 H32 N4 O4 S CSc1ccccc1....
8 6R8L Kd = 0.006 uM JUZ C26 H32 N4 O4 S CSc1ccccc1....
9 6R9U Kd = 7.5 mM JVQ C13 H16 N2 O3 CCN1Cc2cc3....
10 6R9S Kd = 7.1 mM JVN C11 H12 F N O2 c1cc2c(cc1....
70% Homology Family (52)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 20 families.
1 5NOR - 93Q C6 H8 N2 Cc1cccnc1N
2 5T9W Kd = 2600 nM 78E C30 H42 N4 O6 CC(C)[C@H]....
3 5NOV - 93B C4 H8 N2 S C1CNC(=S)N....
4 6X4O Kd = 10 nM UO7 C28 H35 N5 O5 C[C@@H]1c2....
5 5NOS - 92Z C5 H6 N2 O C1C=C(C(=O....
6 4DGB - PRO GLY PRO LEU PRO ALA n/a n/a
7 1W8L Ki = 320 mM 1P3 C8 H15 N O C[C@@H]1CC....
8 5T9U Kd = 25 nM 7HG C34 H50 N4 O8 C[C@H]1[C@....
9 1AWV - HIS VAL GLY PRO ILE ALA n/a n/a
10 5TA2 Kd = 11 nM 78X C36 H48 N4 O7 C[C@@H]1c2....
11 5NOT - 938 C4 H4 Cl N3 c1c(c(ncn1....
12 5T9Z Kd = 64 nM 78R C35 H46 N4 O7 C[C@@H]1[C....
13 5NOX - L97 C5 H5 Cl N2 c1cc(c(nc1....
14 5CYH - GLY PRO n/a n/a
15 2CYH - ALA PRO n/a n/a
16 1AWU - HIS VAL GLY PRO ILE ALA n/a n/a
17 1VBT - ALA ALT PRO PHE NIT n/a n/a
18 5TA4 Kd = 24 nM 838 C30 H44 N4 O6 C[C@@H]1c2....
19 5NOY - 93K C7 H9 N3 O c1cc(c(cc1....
20 1YND ic50 = 3.6 nM SFA C60 H91 N5 O13 CC[C@H]1C[....
21 6X4P Kd = 14 nM UOG C30 H39 N5 O5 C[C@@H]1c2....
22 6X4Q Kd = 9 nM UOJ C31 H39 N5 O5 C[C@@H]1c2....
23 5NOZ - L99 C7 H10 N4 O c1cc(c(cc1....
24 3CYH - SER PRO n/a n/a
25 1NMK ic50 = 5.7 nM SFM C39 H56 N4 O10 C[C@H]1[C@....
26 6X4N Kd = 4 nM UOD C30 H39 N5 O5 C[C@@H]1c2....
27 5NOW - L89 C5 H7 N3 c1cncc(c1N....
28 6X3Y Kd = 10000 nM UMM C28 H42 N4 O7 CC(C)[C@@H....
29 6X4M Kd = 11000 nM UMM C28 H42 N4 O7 CC(C)[C@@H....
30 4CYH - HIS PRO n/a n/a
31 1RMH - SIN ALA ALA PRO PHE NIT n/a n/a
32 1AWR - HIS ALA GLY PRO ILE ALA n/a n/a
33 1AWQ - HIS ALA GLY PRO ILE ALA n/a n/a
34 5LUD - 76X C5 H7 N3 c1cc(c(nc1....
35 1VBS - ALA DAL PRO PHE NIT n/a n/a
36 5NOQ - 93E C5 H5 Cl N2 c1cc(c(nc1....
37 1W8M Ki = 25 mM E1P C9 H15 N O3 CCOC(=O)C(....
38 6X3R Kd = 30000 nM ZXX C22 H32 N4 O6 CC(C)[C@@H....
39 5NOU - L60 C4 H8 N2 O C1CNC(=O)N....
40 6R9X Kd = 1.1 mM JW2 C13 H17 N3 O2 c1ccnc(c1)....
41 4ZSD - 7I6 C24 H32 N4 O2 S2 CSCC[C@@H]....
42 4XNC - EA4 C12 H17 N3 O3 CCOC(=O)CN....
43 4ZSC - EA4 C12 H17 N3 O3 CCOC(=O)CN....
44 6RA1 - JWB C11 H13 N O4 C1C[C@H]2C....
45 6R8W Kd = 1.2 uM JVH C23 H27 N3 O5 c1cc2c(cc1....
46 6R8O Kd = 0.67 uM JV2 C26 H32 N4 O4 S CSc1ccccc1....
47 6R8L Kd = 0.006 uM JUZ C26 H32 N4 O4 S CSc1ccccc1....
48 6R9U Kd = 7.5 mM JVQ C13 H16 N2 O3 CCN1Cc2cc3....
49 6R9S Kd = 7.1 mM JVN C11 H12 F N O2 c1cc2c(cc1....
50 5YBA Kd = 16.81 uM GLU TYR GLY PRO LYS TRP ASN LYS n/a n/a
51 1VDN - ACE ALA ALA PRO ALA MCM n/a n/a
52 1E8K - ALA PRO n/a n/a
50% Homology Family (52)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 13 families.
1 5NOR - 93Q C6 H8 N2 Cc1cccnc1N
2 5T9W Kd = 2600 nM 78E C30 H42 N4 O6 CC(C)[C@H]....
3 5NOV - 93B C4 H8 N2 S C1CNC(=S)N....
4 6X4O Kd = 10 nM UO7 C28 H35 N5 O5 C[C@@H]1c2....
5 5NOS - 92Z C5 H6 N2 O C1C=C(C(=O....
6 4DGB - PRO GLY PRO LEU PRO ALA n/a n/a
7 1W8L Ki = 320 mM 1P3 C8 H15 N O C[C@@H]1CC....
8 5T9U Kd = 25 nM 7HG C34 H50 N4 O8 C[C@H]1[C@....
9 1AWV - HIS VAL GLY PRO ILE ALA n/a n/a
10 5TA2 Kd = 11 nM 78X C36 H48 N4 O7 C[C@@H]1c2....
11 5NOT - 938 C4 H4 Cl N3 c1c(c(ncn1....
12 5T9Z Kd = 64 nM 78R C35 H46 N4 O7 C[C@@H]1[C....
13 5NOX - L97 C5 H5 Cl N2 c1cc(c(nc1....
14 5CYH - GLY PRO n/a n/a
15 2CYH - ALA PRO n/a n/a
16 1AWU - HIS VAL GLY PRO ILE ALA n/a n/a
17 1VBT - ALA ALT PRO PHE NIT n/a n/a
18 5TA4 Kd = 24 nM 838 C30 H44 N4 O6 C[C@@H]1c2....
19 5NOY - 93K C7 H9 N3 O c1cc(c(cc1....
20 1YND ic50 = 3.6 nM SFA C60 H91 N5 O13 CC[C@H]1C[....
21 6X4P Kd = 14 nM UOG C30 H39 N5 O5 C[C@@H]1c2....
22 6X4Q Kd = 9 nM UOJ C31 H39 N5 O5 C[C@@H]1c2....
23 5NOZ - L99 C7 H10 N4 O c1cc(c(cc1....
24 3CYH - SER PRO n/a n/a
25 1NMK ic50 = 5.7 nM SFM C39 H56 N4 O10 C[C@H]1[C@....
26 6X4N Kd = 4 nM UOD C30 H39 N5 O5 C[C@@H]1c2....
27 5NOW - L89 C5 H7 N3 c1cncc(c1N....
28 6X3Y Kd = 10000 nM UMM C28 H42 N4 O7 CC(C)[C@@H....
29 6X4M Kd = 11000 nM UMM C28 H42 N4 O7 CC(C)[C@@H....
30 4CYH - HIS PRO n/a n/a
31 1RMH - SIN ALA ALA PRO PHE NIT n/a n/a
32 1AWR - HIS ALA GLY PRO ILE ALA n/a n/a
33 1AWQ - HIS ALA GLY PRO ILE ALA n/a n/a
34 5LUD - 76X C5 H7 N3 c1cc(c(nc1....
35 1VBS - ALA DAL PRO PHE NIT n/a n/a
36 5NOQ - 93E C5 H5 Cl N2 c1cc(c(nc1....
37 1W8M Ki = 25 mM E1P C9 H15 N O3 CCOC(=O)C(....
38 6X3R Kd = 30000 nM ZXX C22 H32 N4 O6 CC(C)[C@@H....
39 5NOU - L60 C4 H8 N2 O C1CNC(=O)N....
40 6R9X Kd = 1.1 mM JW2 C13 H17 N3 O2 c1ccnc(c1)....
41 4ZSD - 7I6 C24 H32 N4 O2 S2 CSCC[C@@H]....
42 4XNC - EA4 C12 H17 N3 O3 CCOC(=O)CN....
43 4ZSC - EA4 C12 H17 N3 O3 CCOC(=O)CN....
44 6RA1 - JWB C11 H13 N O4 C1C[C@H]2C....
45 6R8W Kd = 1.2 uM JVH C23 H27 N3 O5 c1cc2c(cc1....
46 6R8O Kd = 0.67 uM JV2 C26 H32 N4 O4 S CSc1ccccc1....
47 6R8L Kd = 0.006 uM JUZ C26 H32 N4 O4 S CSc1ccccc1....
48 6R9U Kd = 7.5 mM JVQ C13 H16 N2 O3 CCN1Cc2cc3....
49 6R9S Kd = 7.1 mM JVN C11 H12 F N O2 c1cc2c(cc1....
50 5YBA Kd = 16.81 uM GLU TYR GLY PRO LYS TRP ASN LYS n/a n/a
51 1VDN - ACE ALA ALA PRO ALA MCM n/a n/a
52 1E8K - ALA PRO n/a n/a
Polypharmacology
Similar Ligands (2D)
Ligand no: 1; Ligand: JWB; Similar ligands found: 2
No: Ligand ECFP6 Tc MDL keys Tc
1 JWB 1 1
2 GF1 0.458333 0.863636
Ligand no: 2; Ligand: JVQ; Similar ligands found: 1
No: Ligand ECFP6 Tc MDL keys Tc
1 JVQ 1 1
Similar Ligands (3D)
Ligand no: 1; Ligand: JWB; Similar ligands found: 30
No: Ligand Similarity coefficient
1 LTM 0.8982
2 QMR 0.8953
3 NAG 0.8855
4 GJP 0.8851
5 BM3 0.8843
6 NGA 0.8843
7 54Z 0.8840
8 0FN 0.8805
9 F34 0.8784
10 4RU 0.8783
11 A2G 0.8770
12 27B 0.8759
13 S7J 0.8742
14 BBK 0.8728
15 GDL 0.8724
16 H5B 0.8705
17 DNA 0.8702
18 ZPF 0.8693
19 PRF 0.8684
20 NDG 0.8682
21 FBF 0.8679
22 2CZ 0.8678
23 2KA 0.8669
24 ST3 0.8664
25 CIT 0.8644
26 15N 0.8615
27 3XR 0.8591
28 GNM 0.8559
29 1SV 0.8539
30 0JD 0.8535
Ligand no: 2; Ligand: JVQ; Similar ligands found: 61
No: Ligand Similarity coefficient
1 CTN 0.9167
2 5UD 0.9109
3 PIR 0.9074
4 NOS 0.9061
5 FMB 0.9026
6 56N 0.9025
7 FMC 0.8998
8 URI 0.8994
9 5AD 0.8989
10 DCZ 0.8962
11 DUR 0.8959
12 2J2 0.8933
13 THM 0.8930
14 TBN 0.8895
15 XYA 0.8891
16 GI1 0.8889
17 DNB 0.8867
18 ADN 0.8865
19 AD3 0.8862
20 R8Y 0.8849
21 ZIQ 0.8837
22 TRP 0.8832
23 9DI 0.8828
24 3D1 0.8819
25 SQP 0.8810
26 7QV 0.8780
27 WUB 0.8773
28 ANU 0.8772
29 IMH 0.8770
30 1A5 0.8769
31 5MD 0.8761
32 FM2 0.8761
33 UA2 0.8744
34 5GV 0.8732
35 FM1 0.8731
36 38B 0.8731
37 HBI 0.8717
38 26C 0.8699
39 52B 0.8698
40 4MP 0.8689
41 TIZ 0.8687
42 7R7 0.8680
43 MFR 0.8677
44 4OG 0.8675
45 JVN 0.8674
46 KWQ 0.8673
47 DBS 0.8664
48 2LW 0.8657
49 FUB FUB 0.8654
50 LOT 0.8652
51 SQ4 0.8648
52 G6P 0.8647
53 QJ1 0.8643
54 GI3 0.8625
55 WV7 0.8623
56 CC5 0.8618
57 8UY 0.8614
58 AHR FUB 0.8586
59 QMR 0.8581
60 50C 0.8562
61 MXD 0.8529
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 6R8L; Ligand: JUZ; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 1) in the query (biounit: 6r8l.bio1) has 23 residues
No: Leader PDB Ligand Sequence Similarity
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