Receptor
PDB id Resolution Class Description Source Keywords
6JTC 2.39 Å EC: 3.4.14.- CRYSTAL STRUCTURE OF DIPEPTIDYL PEPTIDASE 11 (DPP11) WITH SH PORPHYROMONAS GINGIVALIS (SPACE) PORPHYROMONAS GINGIVALIS (STRAIN ATCC DSM 20709 / CIP 103683 / JCM 12257 / NCTC 11834 / 2561) DIPEPTIDYL AMINOPEPTIDASE S46 PERIO MICROGRAVITY ANTIMICHYDROLASE
Ref.: FRAGMENT-BASED DISCOVERY OF THE FIRST NONPEPTIDYL I OF AN S46 FAMILY PEPTIDASE. SCI REP V. 9 13587 2019
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
GOL A:801;
 Invalid;
 none;
 submit data
92.094 C3 H8 O3 C(C(C...
C8O B:801;
A:802;
 Valid;
Valid;
 none;
none;
 Ki = 8.45 uM
225.201 C9 H11 N3 O4 c1cc(...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
6JTC 2.39 Å EC: 3.4.14.- CRYSTAL STRUCTURE OF DIPEPTIDYL PEPTIDASE 11 (DPP11) WITH SH PORPHYROMONAS GINGIVALIS (SPACE) PORPHYROMONAS GINGIVALIS (STRAIN ATCC DSM 20709 / CIP 103683 / JCM 12257 / NCTC 11834 / 2561) DIPEPTIDYL AMINOPEPTIDASE S46 PERIO MICROGRAVITY ANTIMICHYDROLASE
Ref.: FRAGMENT-BASED DISCOVERY OF THE FIRST NONPEPTIDYL I OF AN S46 FAMILY PEPTIDASE. SCI REP V. 9 13587 2019
Members (2)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 4 families.
1 6JTB - CIT C6 H8 O7 C(C(=O)O)C....
2 6JTC Ki = 8.45 uM C8O C9 H11 N3 O4 c1cc(c(cc1....
70% Homology Family (4)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 3 families.
1 5JWG - ARG ASP n/a n/a
2 5JWI - ARG GLU n/a n/a
3 6JTB - CIT C6 H8 O7 C(C(=O)O)C....
4 6JTC Ki = 8.45 uM C8O C9 H11 N3 O4 c1cc(c(cc1....
50% Homology Family (6)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 2 families.
1 5JWG - ARG ASP n/a n/a
2 6JTC Ki = 8.45 uM C8O C9 H11 N3 O4 c1cc(c(cc1....
3 3WON Ki = 0.41 mM VAL TYR n/a n/a
4 3WOP - VAL TYR ILE HIS PRO PHE n/a n/a
5 3WOL Ki = 0.41 mM VAL TYR n/a n/a
6 3WOQ - VAL TYR ILE HIS PRO PHE n/a n/a
Polypharmacology
Similar Ligands (2D)
Ligand no: 1; Ligand: C8O; Similar ligands found: 1
No: Ligand ECFP6 Tc MDL keys Tc
1 C8O 1 1
Similar Ligands (3D)
Ligand no: 1; Ligand: C8O; Similar ligands found: 171
No: Ligand Similarity coefficient
1 ST1 0.9140
2 TWO 0.9132
3 XM5 0.9109
4 EY7 0.9108
5 TXW 0.9094
6 4NO 0.9084
7 GHM 0.9071
8 GNV 0.9067
9 OKM 0.9056
10 SER DNF 0.9055
11 DNF SER 0.9053
12 LZB 0.9049
13 NAG 0.9049
14 5SB 0.9040
15 MS0 0.9037
16 BQ5 0.9026
17 CX4 0.9013
18 JTA 0.9005
19 MST 0.8996
20 761 0.8996
21 L1O 0.8989
22 2XY 0.8985
23 OCZ 0.8984
24 K82 0.8979
25 2J9 0.8976
26 878 0.8958
27 018 0.8949
28 60L 0.8947
29 L07 0.8946
30 FUJ 0.8936
31 EV3 0.8930
32 BA5 0.8919
33 NDG 0.8918
34 549 0.8916
35 PQZ 0.8914
36 982 0.8911
37 1X8 0.8910
38 LJW 0.8909
39 020 0.8907
40 5PX 0.8907
41 K3Q 0.8903
42 AO6 0.8893
43 EV2 0.8893
44 GNR 0.8887
45 XG1 0.8884
46 GNJ 0.8877
47 P9I 0.8877
48 5GL 0.8877
49 GNY 0.8876
50 UFO 0.8875
51 Q8G 0.8875
52 GF4 0.8871
53 X0W 0.8867
54 9R5 0.8863
55 EAE 0.8863
56 LP8 0.8857
57 9KZ 0.8856
58 ST4 0.8848
59 9UG 0.8843
60 C09 0.8841
61 52F 0.8835
62 BOQ 0.8833
63 LF5 0.8824
64 HHT 0.8819
65 F2W 0.8818
66 EE8 0.8809
67 FWB 0.8802
68 SG2 0.8793
69 GDL 0.8793
70 F95 0.8791
71 VOH 0.8790
72 0W1 0.8790
73 GTV 0.8786
74 9LI 0.8784
75 7M6 0.8784
76 6VD 0.8784
77 344 0.8782
78 VKE 0.8781
79 I6G 0.8780
80 KWH 0.8778
81 IQ5 0.8776
82 YZ9 0.8776
83 FDR 0.8775
84 7SX 0.8768
85 MUR 0.8764
86 8NX 0.8759
87 67X 0.8758
88 YKG 0.8757
89 DNF 0.8757
90 JXK 0.8756
91 8XQ 0.8752
92 AH6 0.8751
93 P9T 0.8751
94 535 0.8750
95 QX4 0.8746
96 L8J 0.8745
97 D87 0.8744
98 8WO 0.8740
99 DNA 0.8740
100 7I2 0.8737
101 D80 0.8734
102 HHS 0.8732
103 PH2 0.8731
104 AJD 0.8727
105 44V 0.8726
106 XQK 0.8723
107 8HC 0.8719
108 2K8 0.8715
109 4I5 0.8713
110 0FK 0.8709
111 EYM 0.8708
112 RH1 0.8703
113 3XR 0.8703
114 2T6 0.8701
115 GM7 0.8692
116 FPM 0.8689
117 CLI 0.8686
118 KMY 0.8686
119 EYA 0.8683
120 JXW 0.8681
121 V1T 0.8679
122 KWQ 0.8677
123 HHR 0.8670
124 8RK 0.8660
125 D2G 0.8658
126 RVE 0.8656
127 TWB 0.8649
128 H5B 0.8648
129 HNT 0.8648
130 GNM 0.8647
131 TJM 0.8643
132 PLP 0.8643
133 5V6 0.8641
134 SYR 0.8639
135 SBK 0.8636
136 3TV 0.8630
137 Q8D 0.8630
138 3Y7 0.8629
139 3MG 0.8628
140 JG8 0.8625
141 JHY 0.8624
142 DJN 0.8619
143 GI3 0.8616
144 V2Z 0.8616
145 JF1 0.8615
146 IEO 0.8613
147 B62 0.8606
148 ZYQ 0.8606
149 6R8 0.8596
150 5V5 0.8594
151 22T 0.8593
152 Q71 0.8584
153 U7E 0.8584
154 DQU 0.8582
155 7FF 0.8582
156 A2G 0.8579
157 GJS 0.8578
158 28S 0.8575
159 MNS 0.8570
160 2FQ 0.8567
161 NGO 0.8564
162 VXX 0.8563
163 SJK 0.8563
164 XEN 0.8561
165 4AV 0.8560
166 JP2 0.8558
167 JYK 0.8556
168 XHP 0.8554
169 D1G 0.8549
170 GZ8 0.8532
171 AX3 0.8514
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 6JTC; Ligand: C8O; 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: 6jtc.bio1) has 13 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 2; Query (leader) PDB : 6JTC; Ligand: C8O; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 2) in the query (biounit: 6jtc.bio2) has 13 residues
No: Leader PDB Ligand Sequence Similarity
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