Receptor
PDB id Resolution Class Description Source Keywords
7C34 1.94 Å EC: 3.2.1.14 CRYSTAL STRUCTURE OF SERRATIA MARCESCENS CHITINASE B COMPLEX BERBERINE SERRATIA MARCESCENS SERRATIA MARCESCENS CHITINASE B BERBERINE HYDROLASE
Ref.: CRYSTAL STRUCTURE-GUIDED DESIGN OF BERBERINE-BASED CHITINASE INHIBITORS. J ENZYME INHIB MED CHEM V. 35 1937 2020
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
BER B:501;
A:501;
 Valid;
Valid;
 none;
none;
 Ki = 11.79 uM
336.361 C20 H18 N O4 COc1c...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
3WD1 2.3 Å EC: 3.2.1.14 SERRATIA MARCESCENS CHITINASE B COMPLEXED WITH SYN-TRIAZOLE SERRATIA MARCESCENS TIM BARREL HYDROLASE HYDROLASE-HYDROLASE INHIBITOR COMPLEX
Ref.: OBSERVATION OF THE CONTROLLED ASSEMBLY OF PRECLICK COMPONENTS IN THE IN SITU CLICK CHEMISTRY GENERATIO CHITINASE INHIBITOR PROC.NATL.ACAD.SCI.USA V. 110 15892 2013
Members (24)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 22 families.
1 3WD4 ic50 = 0.58 uM A1L C24 H31 N9 O3 [H]/N=C(NC....
2 6JKF Kd = 0.19 uM BV0 C24 H25 N6 O3 CC1=CC=CN2....
3 1UR9 Ki = 1.7 uM GDL PHJ NAG n/a n/a
4 1W1Y ic50 = 2.4 mM TYP C14 H16 N2 O3 c1cc(ccc1C....
5 6JK9 Ki = 0.41 uM BU0 C27 H25 N5 O2 C[C@@H](c1....
6 1H0G - 0AR DPR HSE HIS UN1 n/a n/a
7 1E6N - NAG NAG NAG NAG NAG n/a n/a
8 4Z2H ic50 = 8.3 uM M6A C33 H57 N5 O10 [H]/N=C(NC....
9 4Z2K - M6E C38 H67 N5 O10 [H]/N=C(/N....
10 3WD2 ic50 = 0.58 uM A1L C24 H31 N9 O3 [H]/N=C(NC....
11 1E6Z - NAG NAG n/a n/a
12 7C34 Ki = 11.79 uM BER C20 H18 N O4 COc1ccc2cc....
13 1W1V ic50 = 6.3 mM ALJ C11 H19 N5 O2 C1C[C@H]2C....
14 3WD1 ic50 = 0.022 uM ST7 C37 H41 N11 O4 [H]/N=C(/N....
15 3WD3 ic50 = 0.58 uM A1L C24 H31 N9 O3 [H]/N=C(NC....
16 1H0I - VR0 MEA IAS IAS DAL n/a n/a
17 1E6R - NAA AMI NAA n/a n/a
18 4Z2I ic50 = 0.036 uM M6B C34 H59 N5 O10 [H]/N=C(NC....
19 1O6I Ki = 0.65 mM 0HZ C11 H20 N5 O2 NULL
20 1W1P ic50 = 5 mM GIO C7 H10 N2 O2 C1C[C@H]2C....
21 1W1T ic50 = 1.1 mM CHQ C11 H14 N4 O2 c1c([nH]cn....
22 1UR8 Ki = 45 uM GDL NAG n/a n/a
23 4Z2L - M6F C31 H55 N5 O10 [H]/N=C(NC....
24 1OGG Ki = 6.4 uM NAA AMI NAA n/a n/a
70% Homology Family (24)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 20 families.
1 3WD4 ic50 = 0.58 uM A1L C24 H31 N9 O3 [H]/N=C(NC....
2 6JKF Kd = 0.19 uM BV0 C24 H25 N6 O3 CC1=CC=CN2....
3 1UR9 Ki = 1.7 uM GDL PHJ NAG n/a n/a
4 1W1Y ic50 = 2.4 mM TYP C14 H16 N2 O3 c1cc(ccc1C....
5 6JK9 Ki = 0.41 uM BU0 C27 H25 N5 O2 C[C@@H](c1....
6 1H0G - 0AR DPR HSE HIS UN1 n/a n/a
7 1E6N - NAG NAG NAG NAG NAG n/a n/a
8 4Z2H ic50 = 8.3 uM M6A C33 H57 N5 O10 [H]/N=C(NC....
9 4Z2K - M6E C38 H67 N5 O10 [H]/N=C(/N....
10 3WD2 ic50 = 0.58 uM A1L C24 H31 N9 O3 [H]/N=C(NC....
11 1E6Z - NAG NAG n/a n/a
12 7C34 Ki = 11.79 uM BER C20 H18 N O4 COc1ccc2cc....
13 1W1V ic50 = 6.3 mM ALJ C11 H19 N5 O2 C1C[C@H]2C....
14 3WD1 ic50 = 0.022 uM ST7 C37 H41 N11 O4 [H]/N=C(/N....
15 3WD3 ic50 = 0.58 uM A1L C24 H31 N9 O3 [H]/N=C(NC....
16 1H0I - VR0 MEA IAS IAS DAL n/a n/a
17 1E6R - NAA AMI NAA n/a n/a
18 4Z2I ic50 = 0.036 uM M6B C34 H59 N5 O10 [H]/N=C(NC....
19 1O6I Ki = 0.65 mM 0HZ C11 H20 N5 O2 NULL
20 1W1P ic50 = 5 mM GIO C7 H10 N2 O2 C1C[C@H]2C....
21 1W1T ic50 = 1.1 mM CHQ C11 H14 N4 O2 c1c([nH]cn....
22 1UR8 Ki = 45 uM GDL NAG n/a n/a
23 4Z2L - M6F C31 H55 N5 O10 [H]/N=C(NC....
24 1OGG Ki = 6.4 uM NAA AMI NAA n/a n/a
50% Homology Family (24)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 11 families.
1 3WD4 ic50 = 0.58 uM A1L C24 H31 N9 O3 [H]/N=C(NC....
2 6JKF Kd = 0.19 uM BV0 C24 H25 N6 O3 CC1=CC=CN2....
3 1UR9 Ki = 1.7 uM GDL PHJ NAG n/a n/a
4 1W1Y ic50 = 2.4 mM TYP C14 H16 N2 O3 c1cc(ccc1C....
5 6JK9 Ki = 0.41 uM BU0 C27 H25 N5 O2 C[C@@H](c1....
6 1H0G - 0AR DPR HSE HIS UN1 n/a n/a
7 1E6N - NAG NAG NAG NAG NAG n/a n/a
8 4Z2H ic50 = 8.3 uM M6A C33 H57 N5 O10 [H]/N=C(NC....
9 4Z2K - M6E C38 H67 N5 O10 [H]/N=C(/N....
10 3WD2 ic50 = 0.58 uM A1L C24 H31 N9 O3 [H]/N=C(NC....
11 1E6Z - NAG NAG n/a n/a
12 7C34 Ki = 11.79 uM BER C20 H18 N O4 COc1ccc2cc....
13 1W1V ic50 = 6.3 mM ALJ C11 H19 N5 O2 C1C[C@H]2C....
14 3WD1 ic50 = 0.022 uM ST7 C37 H41 N11 O4 [H]/N=C(/N....
15 3WD3 ic50 = 0.58 uM A1L C24 H31 N9 O3 [H]/N=C(NC....
16 1H0I - VR0 MEA IAS IAS DAL n/a n/a
17 1E6R - NAA AMI NAA n/a n/a
18 4Z2I ic50 = 0.036 uM M6B C34 H59 N5 O10 [H]/N=C(NC....
19 1O6I Ki = 0.65 mM 0HZ C11 H20 N5 O2 NULL
20 1W1P ic50 = 5 mM GIO C7 H10 N2 O2 C1C[C@H]2C....
21 1W1T ic50 = 1.1 mM CHQ C11 H14 N4 O2 c1c([nH]cn....
22 1UR8 Ki = 45 uM GDL NAG n/a n/a
23 4Z2L - M6F C31 H55 N5 O10 [H]/N=C(NC....
24 1OGG Ki = 6.4 uM NAA AMI NAA n/a n/a
Polypharmacology
Similar Ligands (2D)
Ligand no: 1; Ligand: BER; Similar ligands found: 3
No: Ligand ECFP6 Tc MDL keys Tc
1 BER 1 1
2 8KL 0.59596 0.884615
3 DEH 0.447059 0.816327
Similar Ligands (3D)
Ligand no: 1; Ligand: BER; Similar ligands found: 147
No: Ligand Similarity coefficient
1 SLX 0.9551
2 SAU 0.9529
3 CTI 0.9284
4 01I 0.9264
5 4B8 0.9214
6 LU2 0.9187
7 HBO BGC 0.9175
8 6B5 0.9171
9 MYC 0.9160
10 FSE 0.9150
11 QUE 0.9138
12 6FX 0.9121
13 5Z5 0.9119
14 N4N 0.9094
15 DN8 0.9083
16 MYU 0.9076
17 797 0.9067
18 4AJ 0.9065
19 3Q2 0.9037
20 3Q1 0.9030
21 AX1 0.9027
22 124 0.9021
23 785 0.9020
24 801 0.9018
25 6JP 0.9016
26 CUE 0.9000
27 XZ1 0.8998
28 609 0.8996
29 1V8 0.8987
30 AO 0.8962
31 36K 0.8959
32 MT6 0.8955
33 907 0.8954
34 E8Z 0.8927
35 X2L 0.8927
36 MBT 0.8914
37 SDN 0.8913
38 OSJ 0.8905
39 NKH 0.8904
40 BBP 0.8894
41 AGI 0.8890
42 517 0.8880
43 3DL 0.8877
44 338 0.8875
45 6JM 0.8854
46 HUL 0.8851
47 Q7U 0.8847
48 1UT 0.8847
49 1V0 0.8844
50 1UR 0.8843
51 IYX 0.8841
52 IRH 0.8839
53 OSD 0.8832
54 7FC 0.8827
55 3D9 0.8821
56 C9G 0.8811
57 WTI 0.8805
58 DX8 0.8804
59 0NJ 0.8803
60 A64 0.8801
61 MRI 0.8800
62 T21 0.8799
63 6BK 0.8795
64 KMP 0.8792
65 79X 0.8792
66 END 0.8790
67 F13 0.8789
68 HWB 0.8774
69 49J 0.8767
70 130 0.8766
71 A63 0.8765
72 97K 0.8765
73 DQH 0.8764
74 3TI 0.8760
75 3G5 0.8758
76 TNC 0.8757
77 RF2 0.8755
78 E98 0.8754
79 2WF 0.8750
80 27F 0.8748
81 1UZ 0.8746
82 NAR 0.8744
83 122 0.8743
84 STR 0.8741
85 E92 0.8733
86 7G2 0.8732
87 EXQ 0.8730
88 780 0.8725
89 FXE 0.8716
90 696 0.8715
91 J2W 0.8715
92 BRY 0.8714
93 3WL 0.8713
94 OSG 0.8712
95 0RA 0.8711
96 NGV 0.8707
97 9YD 0.8703
98 JV5 0.8701
99 BMZ 0.8700
100 120 0.8680
101 4HG 0.8680
102 E3U 0.8680
103 6WN 0.8676
104 J8D 0.8669
105 29F 0.8666
106 IXM 0.8666
107 NOM 0.8665
108 CR4 0.8660
109 3XL 0.8654
110 L43 0.8652
111 678 0.8644
112 K8W 0.8642
113 EBB 0.8640
114 DY9 0.8632
115 M16 0.8625
116 PLO 0.8622
117 F08 0.8618
118 4P9 0.8611
119 J2Q 0.8610
120 1V1 0.8606
121 802 0.8603
122 334 0.8588
123 INR 0.8584
124 V67 0.8584
125 06R 0.8582
126 20D 0.8581
127 1FJ 0.8580
128 0FZ 0.8578
129 1R5 0.8574
130 F33 0.8571
131 3G6 0.8565
132 F36 0.8565
133 3G8 0.8564
134 TFX 0.8563
135 T5J 0.8562
136 KC5 0.8561
137 BIT 0.8561
138 4BE 0.8547
139 08C 0.8543
140 196 0.8537
141 MKU 0.8532
142 6F3 0.8531
143 6WV 0.8529
144 A73 0.8523
145 1VG 0.8512
146 J45 0.8505
147 EQU 0.8505
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 3WD1; Ligand: ST7; Similar sites found with APoc: 2
This union binding pocket(no: 1) in the query (biounit: 3wd1.bio1) has 72 residues
No: Leader PDB Ligand Sequence Similarity
1 5Y2C NAG NAG NAG NAG NAG 39.6867
2 1NWU NAG NAG NAG NDG 47.7901
Pocket No.: 2; Query (leader) PDB : 3WD1; Ligand: ST7; Similar sites found with APoc: 5
This union binding pocket(no: 2) in the query (biounit: 3wd1.bio2) has 72 residues
No: Leader PDB Ligand Sequence Similarity
1 6JMN BV0 32.7968
2 5Y2C NAG NAG NAG NAG NAG 39.6867
3 6HM1 AO3 42.75
4 1NWU NAG NAG NAG NDG 47.7901
5 6KXL NAG 48.9247
Pocket No.: 3; Query (leader) PDB : 3WD1; Ligand: ST7; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 3) in the query (biounit: 3wd1.bio2) has 72 residues
No: Leader PDB Ligand Sequence Similarity
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