Receptor
PDB id Resolution Class Description Source Keywords
3TDT 2 Å EC: 2.3.1.117 COMPLEX OF TETRAHYDRODIPICOLINATE N-SUCCINYLTRANSFERASE WITH 6-OXOPIMELATE 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
26P A:281;
Valid;
none;
submit data
189.166 C7 H11 N O5 C(C[C...
COA A:280;
Valid;
none;
submit data
767.534 C21 H36 N7 O16 P3 S CC(C)...
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: 26P; Similar ligands found: 27
No: Ligand ECFP6 Tc MDL keys Tc
1 26P 1 1
2 11C 0.606061 0.892857
3 UN1 0.606061 0.892857
4 2NP 0.567568 0.735294
5 API 0.548387 0.827586
6 ORN 0.5 0.65625
7 NPI 0.486486 0.862069
8 NLE 0.485714 0.65625
9 DLY 0.472222 0.636364
10 LYS 0.459459 0.617647
11 DHH 0.459459 0.8
12 2JJ 0.447368 0.666667
13 5OY 0.447368 0.666667
14 KKA 0.446809 0.702703
15 6CL 0.435897 0.8
16 GGL 0.428571 0.857143
17 GLU 0.428571 0.857143
18 DGN 0.428571 0.71875
19 DGL 0.428571 0.857143
20 GLN 0.428571 0.71875
21 HSE 0.424242 0.666667
22 7C3 0.416667 0.71875
23 NVA 0.411765 0.645161
24 HCS 0.411765 0.625
25 ONL 0.405405 0.774194
26 REZ 0.404255 0.742857
27 OOG 0.4 0.678571
Ligand no: 2; 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
Similar Ligands (3D)
Ligand no: 1; Ligand: 26P; Similar ligands found: 192
No: Ligand Similarity coefficient
1 MLY 0.9631
2 CIR 0.9620
3 XRX 0.9597
4 ARG 0.9575
5 NNH 0.9455
6 GGB 0.9441
7 ILO 0.9385
8 EGV 0.9377
9 DAR 0.9374
10 IAR 0.9374
11 6HN 0.9371
12 PML 0.9316
13 HAR 0.9307
14 Z70 0.9301
15 J9Y 0.9301
16 MLZ 0.9281
17 ABH 0.9270
18 EXY 0.9269
19 NMM 0.9255
20 M3L 0.9248
21 E8U 0.9233
22 OJD 0.9219
23 FB6 0.9200
24 5PV 0.9198
25 WT2 0.9179
26 4JK 0.9179
27 11X 0.9144
28 JX7 0.9136
29 GVA 0.9136
30 F98 0.9133
31 VUR 0.9127
32 3KJ 0.9107
33 ZZU 0.9103
34 DNN 0.9094
35 DER 0.9093
36 9J6 0.9088
37 S2C 0.9081
38 AHL 0.9081
39 3YP 0.9077
40 KPV 0.9059
41 NOT 0.9051
42 1PS 0.9051
43 S0A 0.9049
44 TEG 0.9045
45 XRS 0.9041
46 A51 0.9037
47 ALY 0.9024
48 HLP 0.9021
49 LUQ 0.9021
50 XI7 0.9018
51 LPA 0.9013
52 DA2 0.9008
53 GLR 0.9005
54 6J5 0.9002
55 SB7 0.9002
56 DA3 0.9002
57 5AB 0.9001
58 LVD 0.8999
59 DHC 0.8997
60 YOF 0.8996
61 68B 0.8995
62 848 0.8989
63 DAH 0.8982
64 IYR 0.8958
65 HRG 0.8948
66 CLT 0.8947
67 XOG 0.8942
68 ENV 0.8930
69 B41 0.8927
70 PPY 0.8920
71 92G 0.8918
72 L06 0.8917
73 0A1 0.8914
74 KYN 0.8912
75 5TO 0.8910
76 5KJ 0.8907
77 ENW 0.8907
78 Q06 0.8898
79 6C9 0.8896
80 KNA 0.8890
81 FOM 0.8887
82 HC4 0.8882
83 SZ7 0.8881
84 N9J 0.8881
85 RGP 0.8881
86 KAP 0.8879
87 37E 0.8875
88 MF3 0.8874
89 CXP 0.8869
90 TZP 0.8869
91 LPB 0.8869
92 OCA 0.8866
93 4TB 0.8857
94 TRP 0.8854
95 3IP 0.8851
96 DXG 0.8848
97 KPA 0.8847
98 2FM 0.8846
99 GB5 0.8841
100 DXP 0.8838
101 M3P 0.8831
102 4DI 0.8827
103 YIP 0.8821
104 4ZD 0.8821
105 TB8 0.8818
106 FZM 0.8812
107 EN1 0.8806
108 PRO GLY 0.8806
109 IJ6 0.8797
110 LX1 0.8794
111 4TP 0.8794
112 E4P 0.8794
113 O45 0.8793
114 6C8 0.8791
115 MES 0.8791
116 BL0 0.8789
117 2MR 0.8786
118 TOH 0.8781
119 NAL 0.8781
120 QFJ 0.8781
121 011 0.8780
122 7BC 0.8779
123 GRQ 0.8776
124 DHM 0.8768
125 M5P 0.8767
126 1YO 0.8767
127 RLG 0.8765
128 DEZ 0.8756
129 AZM 0.8755
130 MVH 0.8752
131 9GB 0.8751
132 4LV 0.8749
133 HMS 0.8749
134 6FG 0.8747
135 TYC 0.8746
136 PAU 0.8743
137 HL4 0.8739
138 4OG 0.8737
139 1N5 0.8725
140 8CV 0.8724
141 MJW 0.8717
142 4LW 0.8712
143 ATX 0.8711
144 G14 0.8711
145 6C4 0.8709
146 KPC 0.8707
147 D53 0.8701
148 58X 0.8701
149 AOY 0.8696
150 VIO 0.8689
151 PMV 0.8680
152 3H2 0.8677
153 TCA 0.8674
154 DX5 0.8671
155 KDG 0.8671
156 BP7 0.8661
157 P4F 0.8661
158 DDW 0.8659
159 IVL 0.8656
160 7OD 0.8654
161 B3U 0.8653
162 PNP 0.8649
163 Q04 0.8649
164 FHV 0.8640
165 R5P 0.8634
166 3VQ 0.8634
167 SG3 0.8631
168 P80 0.8627
169 5LD 0.8626
170 RA7 0.8623
171 SB9 0.8623
172 X48 0.8621
173 DKA 0.8620
174 3IL 0.8618
175 1HS 0.8617
176 JM2 0.8616
177 HSA 0.8613
178 GZ2 0.8608
179 LTN 0.8604
180 P81 0.8602
181 FXY 0.8599
182 14N 0.8591
183 BSA 0.8589
184 HE8 0.8587
185 4CF 0.8579
186 SLZ 0.8571
187 HIC 0.8568
188 0NX 0.8567
189 VC3 0.8562
190 MP5 0.8561
191 RP3 0.8557
192 PTB 0.8532
Ligand no: 2; Ligand: COA; Similar ligands found: 0
No: Ligand Similarity coefficient
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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