Receptor
PDB id Resolution Class Description Source Keywords
6R9S 2 Å EC: 5.2.1.8 HUMAN CYCLOPHILIN D IN COMPLEX WITH BICYCLIC FRAGMENT 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;
 Invalid;
 none;
 submit data
96.063 O4 S [O-]S...
JVN A:302;
A:301;
 Valid;
Valid;
 none;
none;
 Kd = 7.1 mM
209.217 C11 H12 F N O2 c1cc2...
1PE A:303;
 Invalid;
 none;
 submit data
238.278 C10 H22 O6 C(COC...
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: JVN; Similar ligands found: 1
No: Ligand ECFP6 Tc MDL keys Tc
1 JVN 1 1
Similar Ligands (3D)
Ligand no: 1; Ligand: JVN; Similar ligands found: 141
No: Ligand Similarity coefficient
1 NHG 0.9496
2 0JD 0.9250
3 15N 0.9232
4 2C2 0.9212
5 ZZZ 0.9159
6 NGT 0.9139
7 NGW 0.9139
8 NGO 0.9130
9 JJQ 0.9108
10 RGY 0.9086
11 9RH 0.9082
12 2K8 0.9081
13 BCU 0.9066
14 ICB 0.9061
15 NDG 0.9040
16 7MK 0.9039
17 QMR 0.9037
18 QUS 0.9032
19 5FN 0.8991
20 GC3 0.8976
21 6FZ 0.8960
22 4OG 0.8957
23 TRP 0.8950
24 DEW 0.8934
25 GDL 0.8929
26 FF3 0.8912
27 NAG 0.8891
28 9R5 0.8886
29 LTM 0.8870
30 APG 0.8862
31 PHE 0.8861
32 CTN 0.8852
33 RLG 0.8837
34 54Z 0.8832
35 46M 0.8831
36 NCT 0.8826
37 4V6 0.8823
38 4PN 0.8817
39 78U 0.8816
40 X09 0.8812
41 4YO 0.8809
42 IOP 0.8808
43 HNK 0.8805
44 E01 0.8803
45 5JT 0.8799
46 WS7 0.8797
47 9FL 0.8794
48 ANU 0.8793
49 2L3 0.8791
50 JF1 0.8788
51 M02 0.8783
52 DTR 0.8780
53 0FN 0.8774
54 61M 0.8774
55 4JQ 0.8771
56 PPY 0.8769
57 XXP 0.8763
58 NHT 0.8761
59 NSG 0.8753
60 XX3 0.8751
61 9BF 0.8749
62 HHH 0.8741
63 LOG 0.8739
64 44V 0.8739
65 PH2 0.8733
66 2LB 0.8732
67 DBX 0.8719
68 GNL 0.8718
69 CTL 0.8716
70 15E 0.8715
71 TNX 0.8707
72 MQN 0.8706
73 DUR 0.8698
74 2KA 0.8696
75 M74 0.8692
76 4RU 0.8690
77 SEP 0.8685
78 B5D 0.8684
79 GZQ 0.8683
80 ENO 0.8682
81 SRO 0.8682
82 THM 0.8682
83 8VR 0.8680
84 JVQ 0.8674
85 ROI 0.8671
86 MWP 0.8670
87 SWA 0.8666
88 HFA 0.8666
89 FDR 0.8665
90 TYR 0.8665
91 TTL 0.8662
92 20J 0.8661
93 GJP 0.8658
94 ALN 0.8655
95 DQU 0.8653
96 57O 0.8648
97 OIA 0.8645
98 L13 0.8644
99 SYV 0.8642
100 KBB 0.8641
101 HHR 0.8640
102 OA3 0.8633
103 NVU 0.8630
104 HHT 0.8626
105 EXL 0.8626
106 GCU 0.8625
107 YOF 0.8621
108 CS2 0.8621
109 EN1 0.8621
110 PCS 0.8620
111 G6P 0.8616
112 LNR 0.8614
113 CEG 0.8613
114 3PF 0.8612
115 5VL 0.8611
116 NGA 0.8610
117 3C4 0.8609
118 RP5 0.8606
119 2HQ 0.8604
120 SQ7 0.8604
121 IAC 0.8603
122 92K 0.8603
123 DNB 0.8602
124 J6W 0.8599
125 4VY 0.8595
126 CTE 0.8589
127 S8A 0.8587
128 0OC 0.8585
129 94W 0.8580
130 H7S 0.8580
131 OCZ 0.8572
132 ST2 0.8571
133 HNT 0.8557
134 Q71 0.8554
135 GLC 0.8551
136 MS9 0.8550
137 R8Y 0.8550
138 GF1 0.8539
139 AAN 0.8530
140 5MD 0.8525
141 RMN 0.8509
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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