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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
Ligand no: 1; Ligand: COA; Similar ligands found: 211
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 AMX 0.871795 0.988235
7 30N 0.871795 0.913979
8 CAO 0.871795 0.965909
9 CMX 0.864407 0.976744
10 SCO 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 3KK 0.842975 0.977012
16 FYN 0.842975 1
17 SOP 0.836066 0.977012
18 MCD 0.836066 0.954545
19 OXK 0.836066 0.977012
20 CA6 0.836066 0.885417
21 COK 0.836066 0.977012
22 CO6 0.829268 0.977012
23 NMX 0.829268 0.903226
24 1VU 0.829268 0.965909
25 CMC 0.829268 0.977012
26 CAJ 0.822581 0.954545
27 SCD 0.822581 0.976744
28 2MC 0.822581 0.934066
29 2CP 0.81746 0.965909
30 A1S 0.816 0.977012
31 3HC 0.816 0.988372
32 IVC 0.816 0.988372
33 1HE 0.816 0.955056
34 MLC 0.816 0.977012
35 BCO 0.816 0.977012
36 COD 0.810345 0.988235
37 COO 0.809524 0.977012
38 MCA 0.809524 0.965909
39 CAA 0.809524 0.988372
40 YE1 0.809524 0.965517
41 MC4 0.80315 0.923913
42 SCA 0.80315 0.977012
43 CA8 0.796875 0.885417
44 COF 0.796875 0.955056
45 BYC 0.796875 0.977012
46 COW 0.796875 0.965909
47 3CP 0.796875 0.977012
48 IRC 0.796875 0.988372
49 1GZ 0.796875 0.965909
50 HGG 0.796875 0.977012
51 2KQ 0.796875 0.955056
52 BCA 0.790698 0.965909
53 4CA 0.790698 0.965909
54 FAQ 0.790698 0.977012
55 HXC 0.784615 0.955056
56 GRA 0.784615 0.977012
57 1CV 0.781955 0.977012
58 TGC 0.778626 0.965909
59 2NE 0.772727 0.955056
60 1CZ 0.772727 0.965909
61 CO8 0.772727 0.955056
62 S0N 0.772727 0.954545
63 CIC 0.772727 0.977012
64 DCC 0.766917 0.955056
65 UCC 0.766917 0.955056
66 0FQ 0.766917 0.977012
67 MYA 0.766917 0.955056
68 ST9 0.766917 0.955056
69 4CO 0.766917 0.965909
70 5F9 0.766917 0.955056
71 MFK 0.766917 0.955056
72 01A 0.761194 0.934066
73 0ET 0.761194 0.955056
74 WCA 0.755556 0.955056
75 CS8 0.755556 0.944444
76 UOQ 0.75 0.955056
77 NHW 0.75 0.955056
78 NHM 0.75 0.955056
79 4KX 0.75 0.944444
80 HDC 0.75 0.955056
81 MRR 0.744526 0.955056
82 MRS 0.744526 0.955056
83 HFQ 0.744526 0.955056
84 YNC 0.73913 0.965909
85 DAK 0.73913 0.944444
86 8Z2 0.733813 0.944444
87 NHQ 0.723404 0.988372
88 F8G 0.715278 0.913979
89 1HA 0.713287 0.955056
90 01K 0.708333 0.977012
91 COT 0.703448 0.977012
92 CCQ 0.695652 0.934066
93 CA3 0.693878 0.977012
94 7L1 0.692308 0.965909
95 CA5 0.671053 0.934066
96 UCA 0.666667 0.955056
97 93P 0.666667 0.965909
98 CO7 0.664234 0.977012
99 93M 0.64557 0.965909
100 OXT 0.634146 0.913979
101 5TW 0.607143 0.913979
102 4BN 0.607143 0.913979
103 PAP 0.603604 0.811765
104 JBT 0.598837 0.894737
105 BSJ 0.592814 0.944444
106 HMG 0.581081 0.943182
107 COA PLM 0.573333 0.922222
108 PLM COA 0.573333 0.922222
109 A3P 0.54955 0.8
110 PPS 0.547009 0.752688
111 ASP ASP ASP ILE CMC NH2 0.536585 0.932584
112 0WD 0.521739 0.788889
113 SFC 0.490683 0.955056
114 RFC 0.490683 0.955056
115 191 0.490196 0.865979
116 ACE SER ASP ALY THR NH2 COA 0.483333 0.932584
117 3AM 0.482143 0.788235
118 PTJ 0.48062 0.872093
119 4PS 0.477477 0.682353
120 A22 0.468254 0.813953
121 A2D 0.465517 0.802326
122 PUA 0.462585 0.820225
123 PAJ 0.460938 0.883721
124 ATR 0.459016 0.8
125 SAP 0.459016 0.806818
126 AGS 0.459016 0.806818
127 3OD 0.458015 0.825581
128 ADP 0.453782 0.823529
129 A2R 0.448819 0.813953
130 BA3 0.445378 0.802326
131 OAD 0.442748 0.825581
132 NA7 0.442748 0.858824
133 ATP 0.442623 0.823529
134 HEJ 0.442623 0.823529
135 AP5 0.441667 0.802326
136 B4P 0.441667 0.802326
137 AR6 0.439024 0.802326
138 APR 0.439024 0.802326
139 2A5 0.439024 0.847059
140 5FA 0.439024 0.823529
141 AQP 0.439024 0.823529
142 AN2 0.438017 0.813953
143 AT4 0.438017 0.816092
144 48N 0.435714 0.808989
145 M33 0.434426 0.813953
146 9X8 0.431818 0.806818
147 SRP 0.429688 0.837209
148 ANP 0.428571 0.804598
149 ADQ 0.427481 0.804598
150 YLB 0.426573 0.908046
151 YLP 0.425532 0.886364
152 5AL 0.425197 0.813953
153 7D3 0.425 0.793103
154 AD9 0.424 0.804598
155 APU 0.423611 0.786517
156 7D4 0.422764 0.793103
157 CA0 0.422764 0.804598
158 25L 0.422222 0.813953
159 ATF 0.421875 0.795455
160 F2R 0.421769 0.865169
161 NJP 0.421769 0.806818
162 A2P 0.421488 0.788235
163 A A A 0.421053 0.813953
164 8QN 0.419847 0.813953
165 PNS 0.419643 0.682353
166 ACP 0.419355 0.825581
167 NDP 0.417808 0.788889
168 ACQ 0.417323 0.825581
169 A1R 0.416667 0.882353
170 ATP A A A 0.416058 0.770115
171 A 0.415254 0.8
172 AMP 0.415254 0.8
173 1ZZ 0.414815 0.842697
174 NB8 0.414815 0.808989
175 TXA 0.414815 0.816092
176 FYA 0.414815 0.813953
177 DLL 0.413534 0.793103
178 00A 0.413534 0.758242
179 AHX 0.413534 0.829545
180 PAX 0.412903 0.793478
181 DQV 0.411348 0.813953
182 OMR 0.409722 0.853933
183 9ZD 0.409091 0.818182
184 25A 0.409091 0.802326
185 OOB 0.409091 0.793103
186 9ZA 0.409091 0.818182
187 NPW 0.408163 0.822222
188 6YZ 0.407692 0.825581
189 A A 0.407407 0.781609
190 WAQ 0.407407 0.860465
191 TAT 0.40625 0.816092
192 T99 0.40625 0.816092
193 AMO 0.406015 0.837209
194 4AD 0.406015 0.827586
195 A3R 0.406015 0.882353
196 FA5 0.405797 0.816092
197 YAP 0.405797 0.806818
198 B5Y 0.405797 0.786517
199 TXP 0.405405 0.829545
200 ABM 0.404959 0.781609
201 PRX 0.404762 0.825581
202 ME8 0.404412 0.842697
203 BIS 0.404412 0.818182
204 AFH 0.404255 0.78022
205 J7V 0.403846 0.778947
206 NAI 0.402778 0.777778
207 ODP 0.402685 0.78022
208 DAL AMP 0.401515 0.793103
209 AU1 0.4 0.804598
210 ADX 0.4 0.752688
211 SRA 0.4 0.784091
Ligand no: 2; Ligand: NPI; Similar ligands found: 45
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 GLU 0.53125 0.923077
9 DGL 0.53125 0.923077
10 GGL 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 5OY 0.459459 0.657895
25 ONH 0.459459 0.621622
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 HSE 0.4375 0.709677
32 DAB 0.4375 0.625
33 CIR 0.435897 0.621622
34 KAP 0.435897 0.741935
35 DSD 0.431818 0.657895
36 HCS 0.424242 0.666667
37 NVA 0.424242 0.689655
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 DAS 0.40625 0.785714
43 ASP 0.40625 0.785714
44 5CT 0.404255 0.666667
45 ACA 0.4 0.666667
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: 57
This union binding pocket(no: 1) in the query (biounit: 1kgq.bio1) has 47 residues
No: Leader PDB Ligand Sequence Similarity
1 5SXS AMP 1.82482
2 3SHR CMP 1.82482
3 3IWK NAD 2.18978
4 5LX9 OLB 2.55474
5 5WS9 OXL 2.55474
6 4JJF N2I 2.55474
7 2D24 XYS XYS 3.28467
8 5C8W PCG 3.4965
9 2V9M CIT 3.64964
10 1LSH PLD 3.64964
11 4D52 GXL 4.0146
12 4OFG PCG 4.16667
13 5FUI APY 4.54545
14 2O66 FLC 5.18518
15 2EB5 OXL 5.61798
16 5DYO FLU 5.66038
17 4MOB ADP 5.83942
18 1KZL CRM 6.25
19 5UC4 83S 6.36364
20 4KU7 PCG 6.53595
21 6GE9 ACO 6.56934
22 1NE6 SP1 6.93431
23 5HZ9 5M8 7.40741
24 1LNX URI 7.40741
25 5UF1 FUC GAL NAG 8.09717
26 1J2Z SOG 8.14815
27 1MXG ACR 8.75912
28 6GNO XDI 8.88889
29 3MQG UDP UDP 9.89583
30 3MQG UDP 9.89583
31 3MQG U5P 9.89583
32 3MQG ACO 9.89583
33 3FS8 ACO 10.2564
34 3FS8 TDR 10.2564
35 1SSQ CYS 10.9489
36 2WLG SOP 11.1628
37 4M1U A2G MBG 12.8571
38 3PNA CMP 13.6364
39 2HYQ MAN MAN 17.2131
40 2GUD BMA 17.2131
41 2GUC MAN 17.2131
42 2NU5 NAG 17.2131
43 2HYR BGC GLC 17.2131
44 2GUD MAN 17.2131
45 2NUO BGC 17.2131
46 1KRR ACO 17.8832
47 4MZU COA 17.8832
48 1HV9 COA 18.6131
49 3TWD GOB 18.6131
50 4AAW R84 18.9781
51 3VBK COA 19.0244
52 4EA7 COA 19.3431
53 4EA7 JB2 19.3431
54 3I3X U22 21.1679
55 5T2Y 753 23.2323
56 2QIA U20 23.2824
57 4HZD COA 24.0876
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: 55
This union binding pocket(no: 4) in the query (biounit: 1kgq.bio1) has 48 residues
No: Leader PDB Ligand Sequence Similarity
1 5SXS AMP 1.82482
2 3SHR CMP 1.82482
3 3IWK NAD 2.18978
4 5LX9 OLB 2.55474
5 4JJF N2I 2.55474
6 2D24 XYS XYS 3.28467
7 5C8W PCG 3.4965
8 2V9M CIT 3.64964
9 1LSH PLD 3.64964
10 4D52 GXL 4.0146
11 4OFG PCG 4.16667
12 5FUI APY 4.54545
13 2EB5 OXL 5.61798
14 5DYO FLU 5.66038
15 4MOB ADP 5.83942
16 1KZL CRM 6.25
17 5UC4 83S 6.36364
18 4KU7 PCG 6.53595
19 6GE9 ACO 6.56934
20 1NE6 SP1 6.93431
21 5HZ9 5M8 7.40741
22 1LNX URI 7.40741
23 5UF1 FUC GAL NAG 8.09717
24 1J2Z SOG 8.14815
25 1MXG ACR 8.75912
26 6GNO XDI 8.88889
27 3MQG UDP UDP 9.89583
28 3MQG UDP 9.89583
29 3MQG U5P 9.89583
30 3MQG ACO 9.89583
31 3FS8 ACO 10.2564
32 3FS8 TDR 10.2564
33 1SSQ CYS 10.9489
34 2WLG SOP 11.1628
35 3PNA CMP 13.6364
36 2HYQ MAN MAN 17.2131
37 2GUD BMA 17.2131
38 2GUC MAN 17.2131
39 2NU5 NAG 17.2131
40 2HYR BGC GLC 17.2131
41 2GUD MAN 17.2131
42 2NUO BGC 17.2131
43 1KRR ACO 17.8832
44 4MZU COA 17.8832
45 1HV9 COA 18.6131
46 3TWD GOB 18.6131
47 4AAW R84 18.9781
48 3VBK COA 19.0244
49 3VBK 0FX 19.0244
50 4EA7 JB2 19.3431
51 4EA7 COA 19.3431
52 3I3X U22 21.1679
53 5T2Y 753 23.2323
54 2QIA U20 23.2824
55 4HZD COA 24.0876
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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