Receptor
PDB id Resolution Class Description Source Keywords
5E3R 1.85 Å EC: 2.3.1.117 CRYSTAL STRUCTURE OF DAPD IN COMPLEX WITH 2-AMINOPIMELATE FR CORYNEBACTERIUM GLUTAMICUM CORYNEBACTERIUM GLUTAMICUM TRANSFERASE CORYNEBACTERIUM GLUTAMICUM L-LYSINE
Ref.: CRYSTAL STRUCTURE AND BIOCHEMICAL CHARACTERIZATION TETRAHYDRODIPICOLINATE N-SUCCINYLTRANSFERASE FROM CORYNEBACTERIUM GLUTAMICUM. J.AGRIC.FOOD CHEM. V. 63 10641 2015
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
NPI A:401;
 Valid;
 none;
 submit data
175.182 C7 H13 N O4 C(CCC...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
5E3Q 1.8 Å EC: 2.3.1.117 CRYSTAL STRUCTURE OF DAPD IN COMPLEX WITH SUCCINYL-COA FROM CORYNEBACTERIUM GLUTAMICUM CORYNEBACTERIUM GLUTAMICUM (STRAIN ATCDSM 20300 / JCM 1318 / LMG 3730 / NCIMB 10025) TRANSFERASE CORYNEBACTERIUM GLUTAMICUM L-LYSINE
Ref.: CRYSTAL STRUCTURE AND BIOCHEMICAL CHARACTERIZATION TETRAHYDRODIPICOLINATE N-SUCCINYLTRANSFERASE FROM CORYNEBACTERIUM GLUTAMICUM. J.AGRIC.FOOD CHEM. V. 63 10641 2015
Members (2)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 3 families.
1 5E3Q - SCA C25 H40 N7 O19 P3 S CC(C)(CO[P....
2 5E3R - NPI C7 H13 N O4 C(CCC(=O)O....
70% Homology Family (3)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 2 families.
1 5E3Q - SCA C25 H40 N7 O19 P3 S CC(C)(CO[P....
2 5E3R - NPI C7 H13 N O4 C(CCC(=O)O....
3 3FSY - SCA C25 H40 N7 O19 P3 S CC(C)(CO[P....
50% Homology Family (3)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 2 families.
1 5E3Q - SCA C25 H40 N7 O19 P3 S CC(C)(CO[P....
2 5E3R - NPI C7 H13 N O4 C(CCC(=O)O....
3 3FSY - SCA C25 H40 N7 O19 P3 S CC(C)(CO[P....
Polypharmacology
Similar Ligands (2D)
Ligand no: 1; Ligand: NPI; Similar ligands found: 47
No: Ligand ECFP6 Tc MDL keys Tc
1 NPI 1 1
2 11C 0.677419 0.961538
3 UN1 0.677419 0.961538
4 DLY 0.575758 0.733333
5 API 0.566667 0.888889
6 DHH 0.558824 0.925926
7 LYS 0.558824 0.709677
8 GGL 0.53125 0.923077
9 DGL 0.53125 0.923077
10 GLU 0.53125 0.923077
11 ORN 0.515152 0.7
12 ABH 0.513514 0.625
13 REZ 0.511628 0.787879
14 CBH 0.5 0.83871
15 6HN 0.5 0.619048
16 NLE 0.5 0.7
17 SHR 0.488889 0.83871
18 26P 0.486486 0.862069
19 PML 0.482759 0.666667
20 0L1 0.464286 0.692308
21 ALY 0.463415 0.666667
22 2NP 0.461538 0.78125
23 2JJ 0.459459 0.657895
24 ONH 0.459459 0.621622
25 5OY 0.459459 0.657895
26 EXY 0.452381 0.685714
27 DNN 0.45 0.6875
28 6CL 0.447368 0.857143
29 GLN 0.441176 0.766667
30 DGN 0.441176 0.766667
31 DAB 0.4375 0.625
32 HSE 0.4375 0.709677
33 KAP 0.435897 0.741935
34 CIR 0.435897 0.621622
35 DSD 0.431818 0.657895
36 NVA 0.424242 0.689655
37 HCS 0.424242 0.666667
38 AZ1 0.419355 0.642857
39 3O3 0.418605 0.787879
40 ONL 0.416667 0.766667
41 IKT 0.409091 0.766667
42 CWL 0.409091 0.766667
43 ASP 0.40625 0.785714
44 DAS 0.40625 0.785714
45 5CT 0.404255 0.666667
46 ACA 0.4 0.666667
47 ZGL 0.4 0.741935
Similar Ligands (3D)
Ligand no: 1; Ligand: NPI; Similar ligands found: 205
No: Ligand Similarity coefficient
1 MLY 0.9961
2 ARG 0.9877
3 IAR 0.9833
4 DAR 0.9833
5 ILO 0.9807
6 GGB 0.9745
7 MLZ 0.9698
8 VUR 0.9613
9 M3L 0.9598
10 WT2 0.9500
11 4JK 0.9498
12 NOT 0.9487
13 NMM 0.9470
14 FB6 0.9451
15 HAR 0.9442
16 NNH 0.9427
17 HOC 0.9403
18 ZZU 0.9381
19 AHL 0.9342
20 LPA 0.9338
21 GVA 0.9336
22 OOG 0.9294
23 OCA 0.9284
24 ENV 0.9277
25 LPB 0.9272
26 ENW 0.9270
27 2FM 0.9270
28 S2C 0.9247
29 HRG 0.9239
30 DA3 0.9236
31 011 0.9225
32 RED 0.9221
33 JX7 0.9201
34 5AB 0.9197
35 9J6 0.9168
36 2OR 0.9158
37 3KJ 0.9149
38 8AC 0.9147
39 9YT 0.9144
40 Z70 0.9144
41 DA2 0.9140
42 MF3 0.9138
43 CLT 0.9130
44 4TB 0.9126
45 HC4 0.9114
46 4ZD 0.9110
47 SLZ 0.9106
48 EN1 0.9102
49 E8U 0.9100
50 JM2 0.9088
51 PBN 0.9082
52 RGP 0.9080
53 4DI 0.9075
54 TEG 0.9072
55 LYN 0.9071
56 2MR 0.9065
57 FXY 0.9057
58 S0A 0.9056
59 5PV 0.9055
60 11X 0.9050
61 1PS 0.9050
62 G3M 0.9047
63 XOG 0.9046
64 PUE 0.9031
65 TZP 0.9030
66 LUQ 0.9027
67 KLS 0.9023
68 6FG 0.9017
69 VIO 0.9015
70 CUW 0.9013
71 OJD 0.9008
72 AOY 0.9002
73 1HS 0.8999
74 7XA 0.8996
75 DEZ 0.8993
76 M3P 0.8992
77 2J3 0.8986
78 IJ6 0.8982
79 XRX 0.8976
80 3H2 0.8974
81 SB7 0.8973
82 7UC 0.8967
83 L06 0.8966
84 GRQ 0.8965
85 DDK 0.8961
86 DHC 0.8960
87 Q06 0.8951
88 PMV 0.8944
89 F98 0.8941
90 EGV 0.8937
91 AZM 0.8935
92 KNA 0.8932
93 DKA 0.8932
94 6C8 0.8928
95 DHM 0.8926
96 4TP 0.8926
97 58X 0.8925
98 5TO 0.8922
99 AHN 0.8920
100 DIR 0.8914
101 CXP 0.8911
102 N8C 0.8906
103 SPD 0.8901
104 YIH 0.8897
105 KPC 0.8895
106 PAU 0.8893
107 64Z 0.8890
108 A51 0.8886
109 DLT 0.8884
110 5O5 0.8880
111 OC9 0.8873
112 1N5 0.8868
113 IVL 0.8866
114 8SZ 0.8865
115 3YP 0.8855
116 5KJ 0.8854
117 KPV 0.8852
118 TCA 0.8851
119 PA5 0.8841
120 MHN 0.8839
121 P80 0.8838
122 D53 0.8827
123 I38 0.8825
124 DXP 0.8817
125 QH3 0.8816
126 9GB 0.8814
127 GJK 0.8813
128 GLR 0.8813
129 7C3 0.8811
130 DIA 0.8810
131 DXG 0.8805
132 NWH 0.8803
133 4FE 0.8803
134 HE8 0.8799
135 6C4 0.8797
136 AG2 0.8796
137 ODI 0.8796
138 GLY GLY GLY 0.8793
139 XRS 0.8790
140 QFJ 0.8781
141 MVH 0.8780
142 KDG 0.8779
143 3CX 0.8776
144 37E 0.8776
145 O45 0.8776
146 19N 0.8775
147 E4P 0.8774
148 FER 0.8768
149 FOM 0.8764
150 HPL 0.8764
151 HL4 0.8763
152 D10 0.8760
153 YIP 0.8760
154 DER 0.8749
155 3OL 0.8748
156 R10 0.8745
157 CCU 0.8743
158 SHV 0.8742
159 5LD 0.8739
160 RES 0.8738
161 KPA 0.8736
162 JPQ 0.8733
163 J9Y 0.8732
164 OYA 0.8731
165 E79 0.8730
166 KQY 0.8729
167 A5P 0.8724
168 FB5 0.8724
169 NMH 0.8721
170 M1T 0.8720
171 N6C 0.8716
172 HPO 0.8708
173 HGA 0.8695
174 7OD 0.8695
175 RP3 0.8692
176 HPN 0.8688
177 N9J 0.8687
178 SSB 0.8684
179 SNR 0.8683
180 DX5 0.8670
181 CIY 0.8668
182 5XA 0.8663
183 AE3 0.8657
184 5SP 0.8651
185 6Q3 0.8649
186 5DL 0.8636
187 HSA 0.8635
188 4KJ 0.8628
189 PAN 0.8626
190 DMA 0.8621
191 DZA 0.8616
192 6J5 0.8615
193 5RP 0.8603
194 TX4 0.8601
195 BCH 0.8597
196 S7D 0.8592
197 MGB 0.8591
198 Q9Z 0.8583
199 1X4 0.8568
200 N7I 0.8558
201 4U7 0.8554
202 PTU 0.8554
203 C9M 0.8549
204 0A1 0.8532
205 S8V 0.8520
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 5E3Q; Ligand: SCA; 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: 5e3q.bio1) has 36 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 2; Query (leader) PDB : 5E3Q; Ligand: SCA; 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: 5e3q.bio1) has 36 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 3; Query (leader) PDB : 5E3Q; Ligand: SCA; 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: 5e3q.bio1) has 36 residues
No: Leader PDB Ligand Sequence Similarity
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