Receptor
PDB id Resolution Class Description Source Keywords
2TDT 2 Å EC: 2.3.1.117 COMPLEX OF TETRAHYDRODIPICOLINATE N-SUCCINYLTRANSFERASE WITH AMINOPIMELATE AND COENZYME A MYCOBACTERIUM BOVIS ACYLTRANSFERASE LYSINE BIOSYNTHESIS
Ref.: THE CONFORMATIONAL CHANGE AND ACTIVE SITE STRUCTURE TETRAHYDRODIPICOLINATE N-SUCCINYLTRANSFERASE. BIOCHEMISTRY V. 37 10363 1998
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
COA A:280;
Valid;
none;
submit data
767.534 C21 H36 N7 O16 P3 S CC(C)...
NPI A:281;
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
1KGQ 2 Å EC: 2.3.1.117 CRYSTAL STRUCTURE OF TETRAHYDRODIPICOLINATE N-SUCCINYLTRANSF COMPLEX WITH L-2-AMINOPIMELATE AND SUCCINAMIDE-COA MYCOBACTERIUM BOVIS LEFT-HANDED PARALLEL BETA HELIX TRANSFERASE
Ref.: ACYL GROUP SPECIFICITY AT THE ACTIVE SITE OF TETRAHYDRIDIPICOLINATE N-SUCCINYLTRANSFERASE. PROTEIN SCI. V. 11 974 2002
Members (4)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 3 families.
1 1KGT - SCA C25 H40 N7 O19 P3 S CC(C)(CO[P....
2 3TDT - COA C21 H36 N7 O16 P3 S CC(C)(CO[P....
3 1KGQ - SCO C25 H41 N8 O19 P3 CC(C)(CO[P....
4 2TDT - NPI C7 H13 N O4 C(CCC(=O)O....
70% Homology Family (4)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 2 families.
1 1KGT - SCA C25 H40 N7 O19 P3 S CC(C)(CO[P....
2 3TDT - COA C21 H36 N7 O16 P3 S CC(C)(CO[P....
3 1KGQ - SCO C25 H41 N8 O19 P3 CC(C)(CO[P....
4 2TDT - NPI C7 H13 N O4 C(CCC(=O)O....
50% Homology Family (4)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 2 families.
1 1KGT - SCA C25 H40 N7 O19 P3 S CC(C)(CO[P....
2 3TDT - COA C21 H36 N7 O16 P3 S CC(C)(CO[P....
3 1KGQ - SCO C25 H41 N8 O19 P3 CC(C)(CO[P....
4 2TDT - NPI C7 H13 N O4 C(CCC(=O)O....
Polypharmacology
Similar Ligands (2D)
Ligand no: 1; Ligand: COA; Similar ligands found: 243
No: Ligand ECFP6 Tc MDL keys Tc
1 COA 1 1
2 0T1 0.894737 0.976744
3 DCA 0.893805 0.954023
4 COS 0.887931 0.977012
5 ETB 0.877193 0.920455
6 30N 0.871795 0.913979
7 CAO 0.871795 0.965909
8 AMX 0.871795 0.988235
9 SCO 0.864407 0.976744
10 CMX 0.864407 0.976744
11 ACO 0.857143 0.965909
12 FCX 0.857143 0.94382
13 FAM 0.857143 0.954545
14 HAX 0.85 0.954545
15 FYN 0.842975 1
16 3KK 0.842975 0.977012
17 OXK 0.836066 0.977012
18 KGP 0.836066 0.885417
19 SOP 0.836066 0.977012
20 YZS 0.836066 0.885417
21 COK 0.836066 0.977012
22 MCD 0.836066 0.954545
23 CA6 0.836066 0.885417
24 1VU 0.829268 0.965909
25 CMC 0.829268 0.977012
26 CO6 0.829268 0.977012
27 NMX 0.829268 0.903226
28 CAJ 0.822581 0.954545
29 2MC 0.822581 0.934066
30 SCD 0.822581 0.976744
31 2CP 0.81746 0.965909
32 3HC 0.816 0.988372
33 KGJ 0.816 0.893617
34 A1S 0.816 0.977012
35 MLC 0.816 0.977012
36 BCO 0.816 0.977012
37 IVC 0.816 0.988372
38 1HE 0.816 0.955056
39 COD 0.810345 0.988235
40 CAA 0.809524 0.988372
41 MCA 0.809524 0.965909
42 SO5 0.809524 0.876289
43 YE1 0.809524 0.965517
44 COO 0.809524 0.977012
45 LCV 0.809524 0.876289
46 YXS 0.80315 0.885417
47 MC4 0.80315 0.923913
48 YXR 0.80315 0.885417
49 SCA 0.80315 0.977012
50 KGA 0.796875 0.884211
51 HGG 0.796875 0.977012
52 BYC 0.796875 0.977012
53 3CP 0.796875 0.977012
54 COW 0.796875 0.965909
55 CA8 0.796875 0.885417
56 1GZ 0.796875 0.965909
57 KFV 0.796875 0.894737
58 IRC 0.796875 0.988372
59 COF 0.796875 0.955056
60 2KQ 0.796875 0.955056
61 4CA 0.790698 0.965909
62 FAQ 0.790698 0.977012
63 BCA 0.790698 0.965909
64 HXC 0.784615 0.955056
65 GRA 0.784615 0.977012
66 1CV 0.781955 0.977012
67 TGC 0.778626 0.965909
68 1CZ 0.772727 0.965909
69 S0N 0.772727 0.954545
70 CO8 0.772727 0.955056
71 2NE 0.772727 0.955056
72 CIC 0.772727 0.977012
73 MYA 0.766917 0.955056
74 0FQ 0.766917 0.977012
75 DCC 0.766917 0.955056
76 5F9 0.766917 0.955056
77 UCC 0.766917 0.955056
78 MFK 0.766917 0.955056
79 ST9 0.766917 0.955056
80 4CO 0.766917 0.965909
81 01A 0.761194 0.934066
82 0ET 0.761194 0.955056
83 CS8 0.755556 0.944444
84 WCA 0.755556 0.955056
85 NHW 0.75 0.955056
86 HDC 0.75 0.955056
87 NHM 0.75 0.955056
88 4KX 0.75 0.944444
89 UOQ 0.75 0.955056
90 HFQ 0.744526 0.955056
91 MRS 0.744526 0.955056
92 MRR 0.744526 0.955056
93 J5H 0.73913 0.977012
94 YNC 0.73913 0.965909
95 DAK 0.73913 0.944444
96 COA FLC 0.736 0.965116
97 8Z2 0.733813 0.944444
98 NHQ 0.723404 0.988372
99 F8G 0.715278 0.913979
100 1HA 0.713287 0.955056
101 01K 0.708333 0.977012
102 COT 0.703448 0.977012
103 CCQ 0.695652 0.934066
104 CA3 0.693878 0.977012
105 7L1 0.692308 0.965909
106 RMW 0.682119 0.955056
107 CA5 0.671053 0.934066
108 93P 0.666667 0.965909
109 UCA 0.666667 0.955056
110 CO7 0.664234 0.977012
111 N9V 0.647887 0.922222
112 93M 0.64557 0.965909
113 OXT 0.634146 0.913979
114 4BN 0.607143 0.913979
115 5TW 0.607143 0.913979
116 BUA COA 0.605634 0.943182
117 PAP 0.603604 0.811765
118 JBT 0.598837 0.894737
119 BSJ 0.592814 0.944444
120 6NA COA 0.585034 0.922222
121 HMG 0.581081 0.943182
122 MYR COA 0.573333 0.922222
123 EO3 COA 0.573333 0.922222
124 DAO COA 0.573333 0.922222
125 DCR COA 0.573333 0.922222
126 X90 COA 0.573333 0.922222
127 DKA COA 0.573333 0.922222
128 PLM COA 0.573333 0.922222
129 A3P 0.54955 0.8
130 PPS 0.547009 0.752688
131 ASP ASP ASP ILE NH2 CMC 0.536585 0.932584
132 0WD 0.521739 0.788889
133 SFC 0.490683 0.955056
134 RFC 0.490683 0.955056
135 ACE SER ASP ALY THR NH2 COA 0.483333 0.932584
136 3AM 0.482143 0.788235
137 PTJ 0.48062 0.872093
138 MET VAL ASN ALA CMC 0.480447 0.932584
139 4PS 0.477477 0.682353
140 5AD NJS 0.47619 0.913043
141 A22 0.468254 0.813953
142 A2D 0.465517 0.802326
143 PUA 0.462585 0.820225
144 PAJ 0.460938 0.883721
145 HQG 0.460317 0.813953
146 ATR 0.459016 0.8
147 AGS 0.459016 0.806818
148 3OD 0.458015 0.825581
149 ADP 0.453782 0.823529
150 9BG 0.451389 0.788889
151 A2R 0.448819 0.813953
152 8LE 0.448 0.848837
153 ACE MET LEU GLY PRO NH2 COA 0.447917 0.932584
154 UBG 0.447853 0.844444
155 BA3 0.445378 0.802326
156 OAD 0.442748 0.825581
157 NA7 0.442748 0.858824
158 ATP 0.442623 0.823529
159 HEJ 0.442623 0.823529
160 AP5 0.441667 0.802326
161 B4P 0.441667 0.802326
162 5FA 0.439024 0.823529
163 2A5 0.439024 0.847059
164 APR 0.439024 0.802326
165 AR6 0.439024 0.802326
166 AQP 0.439024 0.823529
167 AT4 0.438017 0.816092
168 AN2 0.438017 0.813953
169 48N 0.435714 0.808989
170 JNT 0.435115 0.847059
171 M33 0.434426 0.813953
172 QA7 0.434109 0.848837
173 8LQ 0.434109 0.837209
174 9X8 0.431818 0.806818
175 SRP 0.429688 0.837209
176 ANP 0.428571 0.804598
177 ADQ 0.427481 0.804598
178 YLB 0.426573 0.908046
179 YLP 0.425532 0.886364
180 5AL 0.425197 0.813953
181 7D3 0.425 0.793103
182 AD9 0.424 0.804598
183 APU 0.423611 0.786517
184 CA0 0.422764 0.804598
185 7D4 0.422764 0.793103
186 25L 0.422222 0.813953
187 ATF 0.421875 0.795455
188 F2R 0.421769 0.865169
189 NJP 0.421769 0.806818
190 A2P 0.421488 0.788235
191 8QN 0.419847 0.813953
192 PNS 0.419643 0.682353
193 ACP 0.419355 0.825581
194 KG4 0.419355 0.804598
195 8LH 0.418605 0.837209
196 J4G 0.41791 0.848837
197 NDP 0.417808 0.788889
198 ACQ 0.417323 0.825581
199 A1R 0.416667 0.882353
200 ATP A 0.416058 0.770115
201 ATP A A A 0.416058 0.770115
202 AMP 0.415254 0.8
203 A 0.415254 0.8
204 1ZZ 0.414815 0.842697
205 TXA 0.414815 0.816092
206 FYA 0.414815 0.813953
207 NB8 0.414815 0.808989
208 00A 0.413534 0.758242
209 DLL 0.413534 0.793103
210 AHX 0.413534 0.829545
211 PAX 0.412903 0.793478
212 DQV 0.411348 0.813953
213 OMR 0.409722 0.853933
214 9ZD 0.409091 0.818182
215 25A 0.409091 0.802326
216 9ZA 0.409091 0.818182
217 OOB 0.409091 0.793103
218 NPW 0.408163 0.822222
219 6YZ 0.407692 0.825581
220 WAQ 0.407407 0.860465
221 TAT 0.40625 0.816092
222 T99 0.40625 0.816092
223 4AD 0.406015 0.827586
224 AMO 0.406015 0.837209
225 A3R 0.406015 0.882353
226 B5Y 0.405797 0.786517
227 FA5 0.405797 0.816092
228 KMQ 0.405797 0.795455
229 TXP 0.405405 0.829545
230 45A 0.404959 0.781609
231 ABM 0.404959 0.781609
232 PRX 0.404762 0.825581
233 ME8 0.404412 0.842697
234 BIS 0.404412 0.818182
235 AFH 0.404255 0.78022
236 J7V 0.403846 0.778947
237 LQJ 0.402878 0.781609
238 NAI 0.402778 0.777778
239 ODP 0.402685 0.78022
240 DAL AMP 0.401515 0.793103
241 SRA 0.4 0.784091
242 ADX 0.4 0.752688
243 AU1 0.4 0.804598
Ligand no: 2; 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: COA; Similar ligands found: 0
No: Ligand Similarity coefficient
Ligand no: 2; 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 : 1KGQ; Ligand: NPI; 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: 1kgq.bio1) has 47 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 2; Query (leader) PDB : 1KGQ; Ligand: NPI; 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: 1kgq.bio1) has 47 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 3; Query (leader) PDB : 1KGQ; Ligand: NPI; 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: 1kgq.bio1) has 47 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 4; Query (leader) PDB : 1KGQ; Ligand: SCO; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 4) in the query (biounit: 1kgq.bio1) has 48 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 5; Query (leader) PDB : 1KGQ; Ligand: SCO; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 5) in the query (biounit: 1kgq.bio1) has 48 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 6; Query (leader) PDB : 1KGQ; Ligand: SCO; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 6) in the query (biounit: 1kgq.bio1) has 48 residues
No: Leader PDB Ligand Sequence Similarity
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