Receptor
PDB id Resolution Class Description Source Keywords
5QYA 1.55 Å NON-ENZYME: OTHER PANDDA ANALYSIS GROUP DEPOSITION -- AAR2/RNASEH IN COMPLEX W FRAGMENT F2X-ENTRY D02A SACCHAROMYCES CEREVISIAE (STRAIN ATCC S288C) FRAGMAX FRAGMAXAPP FRAGMENT SCREENING RNASEH LIKE DOMAINDOMAIN U5 SNRNP ASSEMBLY SPLICING F2X-ENTRY
Ref.: F2X-UNIVERSAL AND F2X-ENTRY: STRUCTURALLY DIVERSE C LIBRARIES FOR CRYSTALLOGRAPHIC FRAGMENT SCREENING. STRUCTURE V. 28 694 2020
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
SY4 B:401;
A:2102;
A:2101;
 Valid;
Valid;
Valid;
 Atoms found MORE than expected: % Diff = 3;
Atoms found MORE than expected: % Diff = 3;
Atoms found MORE than expected: % Diff = 3;
 submit data
250.266 C9 H12 F2 N2 O2 S CCCS(...
PGR A:2104;
A:2105;
 Invalid;
Invalid;
 none;
none;
 submit data
76.094 C3 H8 O2 C[C@H...
SO4 A:2106;
A:2103;
B:402;
 Invalid;
Invalid;
Invalid;
 none;
none;
none;
 submit data
96.063 O4 S [O-]S...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
5R0D 1.27 Å NON-ENZYME: OTHER PANDDA ANALYSIS GROUP DEPOSITION -- AAR2/RNASEH IN COMPLEX W FRAGMENT F2X-ENTRY C11, DMSO-FREE SACCHAROMYCES CEREVISIAE (STRAIN ATCC S288C) FRAGMAX FRAGMAXAPP FRAGMENT SCREENING RNASEH LIKE DOMAINDOMAIN U5 SNRNP ASSEMBLY SPLICING
Ref.: F2X-UNIVERSAL AND F2X-ENTRY: STRUCTURALLY DIVERSE C LIBRARIES FOR CRYSTALLOGRAPHIC FRAGMENT SCREENING. STRUCTURE V. 28 694 2020
Members (35)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1610 families.
1 5R09 - SYG C9 H13 N O CC[C@@H](c....
2 5R0G - SYJ C11 H10 F N O3 S c1ccc(c(c1....
3 5QY1 - R8A C6 H8 N2 O c1cc(c(nc1....
4 5QYB - R9G C12 H15 N O2 COc1cccc(c....
5 5R0B - SY7 C28 H30 N6 O4 COc1cc(ccn....
6 5QYK - SZA C12 H12 N2 O S c1cc(sc1)C....
7 5R0C - R8V C9 H9 N O2 CN1[C@H](c....
8 5QY7 - USJ C9 H11 N O2 CN1[C@H](c....
9 5QYD - R9S C9 H11 N O Cc1ccccc1C....
10 5R0M - SZA C12 H12 N2 O S c1cc(sc1)C....
11 5R0E - SY4 C9 H12 F2 N2 O2 S CCCS(=O)(=....
12 5QYC - SYJ C11 H10 F N O3 S c1ccc(c(c1....
13 5QYJ - TBJ C11 H20 N2 O2 C1CCC(C1)N....
14 5R0J - RBJ C8 H11 N O CNCc1ccc(c....
15 5QY4 - T9S C10 H12 N2 O2 CCOC(=O)N1....
16 5QYI - SZ7 C9 H10 N2 O S c1cc(sc1)/....
17 5R08 - R8A C6 H8 N2 O c1cc(c(nc1....
18 5QYE - USP C8 H10 N2 O2 CN1c2ccc(c....
19 5QY5 - SYA C8 H5 F3 O3 COc1c(c(cc....
20 5R0K - SZ7 C9 H10 N2 O S c1cc(sc1)/....
21 5R0L - TBJ C11 H20 N2 O2 C1CCC(C1)N....
22 5QY3 - SYG C9 H13 N O CC[C@@H](c....
23 5R0H - R9S C9 H11 N O Cc1ccccc1C....
24 5QYH - T9V C9 H11 N O2 CC(=O)Nc1c....
25 5QY6 - SY7 C28 H30 N6 O4 COc1cc(ccn....
26 5QY2 - TJ1 C5 H8 N2 O2 CC(C)C1=NO....
27 5R0D - R8Y C10 H13 N O3 S CCN(CCC(=O....
28 5QYG - RBJ C8 H11 N O CNCc1ccc(c....
29 5QY8 - TJV C8 H7 N O2 S c1cc2c(cc1....
30 5R0I - SYV C8 H8 N2 O2 CN1c2ccc(c....
31 5R0F - R9G C12 H15 N O2 COc1cccc(c....
32 5QY9 - R8Y C10 H13 N O3 S CCN(CCC(=O....
33 5QYF - T9Y C7 H7 F3 N2 O2 CCOC(=O)c1....
34 5QYA - SY4 C9 H12 F2 N2 O2 S CCCS(=O)(=....
35 5R0A - SYA C8 H5 F3 O3 COc1c(c(cc....
70% Homology Family (35)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1331 families.
1 5R09 - SYG C9 H13 N O CC[C@@H](c....
2 5R0G - SYJ C11 H10 F N O3 S c1ccc(c(c1....
3 5QY1 - R8A C6 H8 N2 O c1cc(c(nc1....
4 5QYB - R9G C12 H15 N O2 COc1cccc(c....
5 5R0B - SY7 C28 H30 N6 O4 COc1cc(ccn....
6 5QYK - SZA C12 H12 N2 O S c1cc(sc1)C....
7 5R0C - R8V C9 H9 N O2 CN1[C@H](c....
8 5QY7 - USJ C9 H11 N O2 CN1[C@H](c....
9 5QYD - R9S C9 H11 N O Cc1ccccc1C....
10 5R0M - SZA C12 H12 N2 O S c1cc(sc1)C....
11 5R0E - SY4 C9 H12 F2 N2 O2 S CCCS(=O)(=....
12 5QYC - SYJ C11 H10 F N O3 S c1ccc(c(c1....
13 5QYJ - TBJ C11 H20 N2 O2 C1CCC(C1)N....
14 5R0J - RBJ C8 H11 N O CNCc1ccc(c....
15 5QY4 - T9S C10 H12 N2 O2 CCOC(=O)N1....
16 5QYI - SZ7 C9 H10 N2 O S c1cc(sc1)/....
17 5R08 - R8A C6 H8 N2 O c1cc(c(nc1....
18 5QYE - USP C8 H10 N2 O2 CN1c2ccc(c....
19 5QY5 - SYA C8 H5 F3 O3 COc1c(c(cc....
20 5R0K - SZ7 C9 H10 N2 O S c1cc(sc1)/....
21 5R0L - TBJ C11 H20 N2 O2 C1CCC(C1)N....
22 5QY3 - SYG C9 H13 N O CC[C@@H](c....
23 5R0H - R9S C9 H11 N O Cc1ccccc1C....
24 5QYH - T9V C9 H11 N O2 CC(=O)Nc1c....
25 5QY6 - SY7 C28 H30 N6 O4 COc1cc(ccn....
26 5QY2 - TJ1 C5 H8 N2 O2 CC(C)C1=NO....
27 5R0D - R8Y C10 H13 N O3 S CCN(CCC(=O....
28 5QYG - RBJ C8 H11 N O CNCc1ccc(c....
29 5QY8 - TJV C8 H7 N O2 S c1cc2c(cc1....
30 5R0I - SYV C8 H8 N2 O2 CN1c2ccc(c....
31 5R0F - R9G C12 H15 N O2 COc1cccc(c....
32 5QY9 - R8Y C10 H13 N O3 S CCN(CCC(=O....
33 5QYF - T9Y C7 H7 F3 N2 O2 CCOC(=O)c1....
34 5QYA - SY4 C9 H12 F2 N2 O2 S CCCS(=O)(=....
35 5R0A - SYA C8 H5 F3 O3 COc1c(c(cc....
50% Homology Family (35)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1144 families.
1 5R09 - SYG C9 H13 N O CC[C@@H](c....
2 5R0G - SYJ C11 H10 F N O3 S c1ccc(c(c1....
3 5QY1 - R8A C6 H8 N2 O c1cc(c(nc1....
4 5QYB - R9G C12 H15 N O2 COc1cccc(c....
5 5R0B - SY7 C28 H30 N6 O4 COc1cc(ccn....
6 5QYK - SZA C12 H12 N2 O S c1cc(sc1)C....
7 5R0C - R8V C9 H9 N O2 CN1[C@H](c....
8 5QY7 - USJ C9 H11 N O2 CN1[C@H](c....
9 5QYD - R9S C9 H11 N O Cc1ccccc1C....
10 5R0M - SZA C12 H12 N2 O S c1cc(sc1)C....
11 5R0E - SY4 C9 H12 F2 N2 O2 S CCCS(=O)(=....
12 5QYC - SYJ C11 H10 F N O3 S c1ccc(c(c1....
13 5QYJ - TBJ C11 H20 N2 O2 C1CCC(C1)N....
14 5R0J - RBJ C8 H11 N O CNCc1ccc(c....
15 5QY4 - T9S C10 H12 N2 O2 CCOC(=O)N1....
16 5QYI - SZ7 C9 H10 N2 O S c1cc(sc1)/....
17 5R08 - R8A C6 H8 N2 O c1cc(c(nc1....
18 5QYE - USP C8 H10 N2 O2 CN1c2ccc(c....
19 5QY5 - SYA C8 H5 F3 O3 COc1c(c(cc....
20 5R0K - SZ7 C9 H10 N2 O S c1cc(sc1)/....
21 5R0L - TBJ C11 H20 N2 O2 C1CCC(C1)N....
22 5QY3 - SYG C9 H13 N O CC[C@@H](c....
23 5R0H - R9S C9 H11 N O Cc1ccccc1C....
24 5QYH - T9V C9 H11 N O2 CC(=O)Nc1c....
25 5QY6 - SY7 C28 H30 N6 O4 COc1cc(ccn....
26 5QY2 - TJ1 C5 H8 N2 O2 CC(C)C1=NO....
27 5R0D - R8Y C10 H13 N O3 S CCN(CCC(=O....
28 5QYG - RBJ C8 H11 N O CNCc1ccc(c....
29 5QY8 - TJV C8 H7 N O2 S c1cc2c(cc1....
30 5R0I - SYV C8 H8 N2 O2 CN1c2ccc(c....
31 5R0F - R9G C12 H15 N O2 COc1cccc(c....
32 5QY9 - R8Y C10 H13 N O3 S CCN(CCC(=O....
33 5QYF - T9Y C7 H7 F3 N2 O2 CCOC(=O)c1....
34 5QYA - SY4 C9 H12 F2 N2 O2 S CCCS(=O)(=....
35 5R0A - SYA C8 H5 F3 O3 COc1c(c(cc....
Polypharmacology
Similar Ligands (2D)
Ligand no: 1; Ligand: SY4; Similar ligands found: 1
No: Ligand ECFP6 Tc MDL keys Tc
1 SY4 1 1
Similar Ligands (3D)
Ligand no: 1; Ligand: SY4; Similar ligands found: 131
No: Ligand Similarity coefficient
1 TR7 0.9258
2 LTN 0.9231
3 TRP 0.9216
4 IC9 0.9182
5 ASE 0.9179
6 DUR 0.9152
7 5MD 0.9149
8 JYE 0.9144
9 IOS 0.9092
10 THM 0.9040
11 JY2 0.9022
12 3AD 0.9013
13 8U3 0.9001
14 CTE 0.8984
15 B86 0.8980
16 AC2 0.8975
17 JYW 0.8971
18 9UL 0.8960
19 PF1 0.8959
20 FMC 0.8954
21 IOP 0.8951
22 B41 0.8948
23 HWH 0.8947
24 7MX 0.8947
25 ZON 0.8942
26 H7S 0.8942
27 XJ2 0.8941
28 QH3 0.8941
29 THU 0.8940
30 NIY 0.8938
31 F01 0.8932
32 JXT 0.8923
33 DTR 0.8918
34 ID2 0.8916
35 5WN 0.8916
36 NWD 0.8915
37 7MK 0.8909
38 M3Q 0.8909
39 8XL 0.8904
40 ZEB 0.8902
41 ADN 0.8902
42 1QP 0.8894
43 CTN 0.8886
44 CC5 0.8885
45 5AD 0.8860
46 9BF 0.8849
47 4OG 0.8841
48 EXR 0.8839
49 TYR 0.8833
50 L5E 0.8824
51 BQ2 0.8823
52 URI 0.8821
53 YF3 0.8813
54 F16 0.8811
55 TYU 0.8811
56 NOS 0.8809
57 2TU 0.8806
58 MQG 0.8804
59 SYE 0.8803
60 GOE 0.8803
61 DCZ 0.8802
62 DEW 0.8798
63 ML1 0.8793
64 IPD 0.8776
65 MDR 0.8773
66 3D1 0.8771
67 ZIQ 0.8769
68 FWD 0.8769
69 8HG 0.8769
70 ALN 0.8766
71 RQD 0.8766
72 DTE 0.8763
73 DDU 0.8762
74 CWD 0.8758
75 GNG 0.8754
76 JGB 0.8751
77 8DA 0.8751
78 QTG 0.8733
79 BWD 0.8726
80 0XR 0.8721
81 5FD 0.8716
82 NCV 0.8715
83 MTA 0.8712
84 5N5 0.8707
85 5UD 0.8703
86 IAC 0.8701
87 ALE 0.8693
88 TYE 0.8688
89 9DI 0.8681
90 IWD 0.8678
91 EGR 0.8668
92 W29 0.8668
93 DTY 0.8668
94 EXL 0.8667
95 AD3 0.8664
96 VYM 0.8663
97 NVU 0.8660
98 LLG 0.8658
99 4UO 0.8658
100 GMP 0.8654
101 TBN 0.8644
102 CEG 0.8642
103 MCY 0.8638
104 L12 0.8638
105 57O 0.8636
106 A4D 0.8633
107 2FD 0.8631
108 BNX 0.8625
109 JF1 0.8623
110 MTH 0.8623
111 I2E 0.8621
112 HNM 0.8621
113 79W 0.8618
114 6U5 0.8617
115 R4E 0.8611
116 5I5 0.8611
117 2B4 0.8611
118 IMH 0.8598
119 9B3 0.8597
120 5CD 0.8594
121 JYK 0.8591
122 28N 0.8586
123 UA2 0.8583
124 HNL 0.8581
125 AP4 0.8575
126 SLY 0.8562
127 DHY 0.8561
128 2C2 0.8558
129 GNR 0.8554
130 7FF 0.8542
131 YOF 0.8540
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 5R0D; Ligand: R8Y; 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: 5r0d.bio1) has 23 residues
No: Leader PDB Ligand Sequence Similarity
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