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Receptor
PDB id Resolution Class Description Source Keywords
3I7S 2.3 Å EC: 4.2.1.52 DIHYDRODIPICOLINATE SYNTHASE MUTANT - K161A - WITH THE SUBST PYRUVATE BOUND IN THE ACTIVE SITE. ESCHERICHIA COLI K-12 DIHYDRODIPICOLINATE SYNTHYASE LYSINE BIOSYNTHESIS AMINO-ACBIOSYNTHESIS DIAMINOPIMELATE BIOSYNTHESIS LYASE SCHIFF B
Ref.: HOW ESSENTIAL IS THE 'ESSENTIAL' ACTIVE-SITE LYSINE DIHYDRODIPICOLINATE SYNTHASE? BIOCHIMIE V. 92 837 2010
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
GOL A:293;
A:294;
A:297;
B:293;
B:294;
B:297;
B:300;
B:301;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
none;
none;
none;
none;
none;
none;
none;
none;
submit data
92.094 C3 H8 O3 C(C(C...
K A:295;
A:296;
B:295;
B:296;
B:298;
B:299;
Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
none;
none;
none;
none;
none;
none;
submit data
39.098 K [K+]
PO4 A:299;
A:300;
B:303;
Invalid;
Invalid;
Invalid;
none;
none;
none;
submit data
94.971 O4 P [O-]P...
PYR A:298;
B:302;
Valid;
Valid;
none;
none;
Kd = 0.0299 mM
88.062 C3 H4 O3 CC(=O...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
3I7S 2.3 Å EC: 4.2.1.52 DIHYDRODIPICOLINATE SYNTHASE MUTANT - K161A - WITH THE SUBST PYRUVATE BOUND IN THE ACTIVE SITE. ESCHERICHIA COLI K-12 DIHYDRODIPICOLINATE SYNTHYASE LYSINE BIOSYNTHESIS AMINO-ACBIOSYNTHESIS DIAMINOPIMELATE BIOSYNTHESIS LYASE SCHIFF B
Ref.: HOW ESSENTIAL IS THE 'ESSENTIAL' ACTIVE-SITE LYSINE DIHYDRODIPICOLINATE SYNTHASE? BIOCHIMIE V. 92 837 2010
Members (2)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1 families.
1 1YXD ic50 ~ 0.5 mM LYS C6 H15 N2 O2 C(CC[NH3+]....
2 3I7S Kd = 0.0299 mM PYR C3 H4 O3 CC(=O)C(=O....
70% Homology Family (2)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1 families.
1 1YXD ic50 ~ 0.5 mM LYS C6 H15 N2 O2 C(CC[NH3+]....
2 3I7S Kd = 0.0299 mM PYR C3 H4 O3 CC(=O)C(=O....
50% Homology Family (4)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1 families.
1 5F1U ic50 = 400 nM 3VN C14 H30 N4 O4 C(CCN)C[C@....
2 5F1V Ki ~ 200 nM 3VN C14 H30 N4 O4 C(CCN)C[C@....
3 1YXD ic50 ~ 0.5 mM LYS C6 H15 N2 O2 C(CC[NH3+]....
4 3I7S Kd = 0.0299 mM PYR C3 H4 O3 CC(=O)C(=O....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: PYR; Similar ligands found: 7
No: Ligand ECFP6 Tc MDL keys Tc
1 PYR 1 1
2 ACY 0.636364 0.636364
3 OXD 0.545455 0.642857
4 F50 0.428571 0.6
5 2KT 0.411765 0.733333
6 AAE 0.411765 0.625
7 KIV 0.411765 0.785714
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 3I7S; Ligand: PYR; Similar sites found with APoc: 261
This union binding pocket(no: 1) in the query (biounit: 3i7s.bio1) has 9 residues
No: Leader PDB Ligand Sequence Similarity
1 2OBF SAH 1.38408
2 2OBF F83 1.38408
3 4A0M NAD 1.71233
4 5EHS 5OY 1.86567
5 5EHS 2JJ 1.86567
6 3EKK GS2 2.05479
7 4LZJ 22H 2.05479
8 3D9F FAD 2.05479
9 2C0U FAD NBT 2.05479
10 3D9F N6C 2.05479
11 5EB4 FAD 2.05479
12 5LY3 ADP 2.05479
13 4C2W ANP 2.15054
14 3ZYR NAG NAG BMA MAN MAN NAG NAG 2.29885
15 3ZYR ASN NAG NAG BMA MAN MAN NAG NAG 2.29885
16 1QG6 NAD 2.29885
17 1QG6 TCL 2.29885
18 2J0V GDP 2.35849
19 3AXB FAD 2.39726
20 3WQT ANP 2.39726
21 6FP4 FAD 2.39726
22 6FP4 E1T 2.39726
23 6ER9 FAD 2.39726
24 4RJK TPP 2.39726
25 3O0Q ADN 2.39726
26 3O0Q GDP 2.39726
27 3O0Q TTP 2.39726
28 1GZ4 ATP 2.39726
29 3ZNN 4WL 2.39726
30 3ZNN FAD 2.39726
31 3NYQ AMP 2.39726
32 3KJS NAP 2.39726
33 5EYY MDM 2.44898
34 4EWH T77 2.54545
35 1EX7 5GP 2.68817
36 5KBZ 3B2 2.73973
37 3B9A NAG NAG NAG NAG NAG NAG 2.73973
38 4PIV NDP 2.73973
39 3RHJ NAP 2.73973
40 5THZ SAH 2.73973
41 4A1O JLN 2.73973
42 2XCU C5P 2.73973
43 4NZN ANP 2.73973
44 4NZN 2OU 2.73973
45 6BA2 7KM 2.73973
46 3LDW ZOL 2.73973
47 3LDW IPE 2.73973
48 5ESO ISC 2.73973
49 5ESO TDP 2.73973
50 1HYE NAP 2.73973
51 4NW6 2NS 3.08219
52 3A4V PYR 3.08219
53 3A4V NAD 3.08219
54 1KNR FAD 3.08219
55 4TX6 38B 3.08219
56 4RVG SAM 3.08219
57 1JV1 UD1 3.08219
58 5T67 SAH 3.08219
59 5T67 JHZ 3.08219
60 1NE7 AGP 3.11419
61 1KHT AMP 3.125
62 2NU8 COA 3.125
63 2PHR MAN MAN 3.1746
64 2PHW MAN MAN 3.1746
65 2AUY NAG MAN MMA 3.1746
66 2PHF MAN MAN 3.1746
67 2GND MAN MMA 3.1746
68 2AR6 NAG MAN 3.1746
69 1Q8P MAN MMA 3.1746
70 2GNM MAN 3.1746
71 2PHT MAN MAN MAN 3.1746
72 2PHW MAN MAN MAN BMA MAN MAN MAN 3.1746
73 1UKG MMA 3.1746
74 2PHX MAN MAN MAN MAN 3.1746
75 2PHF MAN MAN BMA MAN 3.1746
76 1Q8Q MAN MMA 3.1746
77 2PHU MAN MAN MAN BMA MAN 3.1746
78 2PHT MAN MAN MAN BMA MAN 3.1746
79 2PHR MAN MAN BMA MAN 3.1746
80 1Q8V MAN MAN MAN 3.1746
81 2AR6 NAG MAN MAN MAN NAG 3.1746
82 1Q8S MAN MMA 3.1746
83 2PHX MAN MAN 3.1746
84 1Q8V MAN MAN 3.1746
85 1Q8O MAN MMA 3.1746
86 1XKQ NDP 3.21429
87 3ENV ABF 3.40426
88 5Y1G AKB 3.42466
89 5Y1G NAD 3.42466
90 1YNH SUO 3.42466
91 4Z0H NAD 3.42466
92 5XWV NDP 3.42466
93 5EXW 7DT 3.42466
94 4Z24 FAD 3.42466
95 3QKT ANP 3.42466
96 4TQK NAG 3.42466
97 4R5M NAP 3.42466
98 4R5M 4NO 3.42466
99 1TPY SAH 3.48432
100 6GFK SAH 3.58566
101 1O8B ABF 3.65297
102 1LLO NAA NAA AMI 3.663
103 4XUC SAM 3.66972
104 4XUC 43G 3.66972
105 2BTO GTP 3.7037
106 4GNI ATP 3.76712
107 2NXW TPP 3.76712
108 4B9Q ATP 3.76712
109 4JNE ATP 3.76712
110 3EYA TDP 3.76712
111 5XVS NAG 3.76712
112 5OBU ANP 3.76712
113 5OBY ANP 3.76712
114 3ETG GWD 3.76712
115 1CER NAD 3.76712
116 2QMC GTB 3.76712
117 3N17 NAG NAG 3.76712
118 2X32 OTP 3.91061
119 4WOP CTP 4
120 5T2Z 017 4.0404
121 5K0A FAD 4.10959
122 2YYE APC 4.10959
123 2NVK FAD 4.10959
124 4WAS NAP 4.10959
125 4HA6 FAD 4.10959
126 2IV3 UDP 4.10959
127 4AZW SAM 4.10959
128 3NUB UD0 4.10959
129 2Q4H AMP 4.10959
130 2B4R AES 4.10959
131 2B4R NAD 4.10959
132 2Z6J FMN 4.10959
133 1N9G NAP 4.10959
134 1KPH SAH 4.18118
135 1KPG SAH 4.18118
136 1E3W NAD 4.21456
137 1E6W NAD 4.23077
138 2RI1 GLP 4.25532
139 3DR4 G4M 4.34783
140 4EHU ANP 4.34783
141 1ERB ETR 4.37158
142 2C94 TSF 4.375
143 2FAV APR 4.44444
144 1FEC FAD 4.45205
145 2YYY NAP 4.45205
146 1RM0 D6P 4.45205
147 3MKH FAD 4.45205
148 3WMX NAD 4.45205
149 5O74 GDP 4.56853
150 2HKA C3S 4.61538
151 2F5Z FAD 4.6875
152 4N9I PCG 4.7619
153 1KOJ PAN 4.79452
154 2C6Q IMP 4.79452
155 4NST ADP 4.79452
156 5X20 NAD 4.79452
157 5I7A 68Q 4.90798
158 1LOF MAN BMA NAG NAG MAN NAG GAL GAL 4.97238
159 4CE5 PDG 5.13699
160 4AF0 IMP 5.13699
161 4Z0G 5GP 5.13699
162 5GM1 SAH 5.13699
163 3CTY FAD 5.32915
164 1P0Z FLC 5.34351
165 1J3I NDP 5.35714
166 5H81 NAP 5.39846
167 1B9I PXG 5.41237
168 5I7S NAD 5.43478
169 5I7S E9P 5.43478
170 1RYI FAD 5.47945
171 1RYI GOA 5.47945
172 1BZL FAD 5.47945
173 1BZL GCG 5.47945
174 3NW7 LGV 5.47945
175 5NII FAD 5.47945
176 2VVL FAD 5.47945
177 4BJ8 BTN 5.55556
178 3NYC IAR 5.82192
179 3NYC FAD 5.82192
180 6A0S HSE 5.82192
181 6A0S NDP 5.82192
182 1PMO PLR 5.82192
183 5I8T LAC 6.14525
184 5UAV NDP 6.16438
185 5UAV TFB 6.16438
186 3ZIA ADP 6.16438
187 3BAZ NAP 6.16438
188 1JQ3 AAT 6.16438
189 3HRD MCN 6.25
190 3OU2 SAH 6.42202
191 2R4J 13P 6.50685
192 2R4J FAD 6.50685
193 5H68 AGS 6.50685
194 5EXE 5SR 6.50685
195 1IK4 PGH 6.57895
196 2YQS UD1 6.84932
197 1YBH P22 6.84932
198 5TI9 NFK 6.84932
199 1ZAP A70 6.84932
200 1W6S PQQ 6.84932
201 3V1Y NAD 6.84932
202 3NDJ JHZ 6.84932
203 3NDJ SAH 6.84932
204 3QFA FAD 6.89655
205 1XVB BHL 7.05882
206 1T9D P22 7.19178
207 5WKC TP9 7.19178
208 3OTX AP5 7.19178
209 4DHY GLC 7.19178
210 4D42 W0I 7.44681
211 4D42 NAP 7.44681
212 2RAB FAD 7.53425
213 4JDR FAD 7.53425
214 3LAD FAD 7.87671
215 2P53 NNG 8.21918
216 5EOU ATP 8.21918
217 3TWO NDP 8.56164
218 1ELU PDA 8.56164
219 3WGT FAD 8.90411
220 3A4X NAG NAG NAG NDG 8.90411
221 3WGT QSC 8.90411
222 4QYN RTL 9.02256
223 3QV1 NAD 9.19881
224 5FBN 5WF 9.22509
225 4LY9 S6P 9.24658
226 4LY9 1YY 9.24658
227 2WK2 SN5 SN5 9.24658
228 2WK2 SN5 SN5 NGT 9.24658
229 2WYV NAD 9.57854
230 2QWO ADP 9.78261
231 5U8U FAD 9.93151
232 1XOC VAL ASP SER LYS ASN THR SER SER TRP 9.93151
233 2DBZ NAP 9.93151
234 5EYP GTP 10.0592
235 3RNM FAD 10.3448
236 2BL9 NDP 10.5042
237 2BL9 CP6 10.5042
238 4J56 FAD 10.5263
239 2VBF TPP 10.6164
240 1T36 ORN 10.6164
241 3QM1 ZYC 10.9434
242 1M0S CIT 11.4155
243 3R5T VBN 11.6438
244 1JAY NAP 11.7925
245 6G3R ADP 12.3288
246 5AR0 GB8 12.3288
247 1RDT L79 12.8099
248 5YJF 8WO 13.7324
249 5YJF SAH 13.7324
250 1LK7 DER 14.4105
251 4QTU SAM 14.4231
252 1XSE NDP 15.5932
253 2FMD MAN MAN 16.25
254 5ITZ GTP 16.2791
255 4MUV PCG 17.6056
256 2V7Q ADP 19.1781
257 1V59 FAD 22.2603
258 1UJ5 5RP 22.9075
259 5KZD RCJ 34.589
260 1F74 NAY 36.9863
261 4IMG NGF 41.4384
Pocket No.: 2; Query (leader) PDB : 3I7S; Ligand: PYR; Similar sites found with APoc: 155
This union binding pocket(no: 2) in the query (biounit: 3i7s.bio1) has 10 residues
No: Leader PDB Ligand Sequence Similarity
1 4XDA RIB 1.36986
2 4XDA ADP 1.36986
3 4R74 F6P 1.71233
4 3RUV ANP 1.71233
5 3OIX FMN 1.71233
6 2H92 C5P 1.82648
7 4X9M FAD 2.05479
8 6ECT SAM 2.05479
9 1WP4 NDP 2.07612
10 2CVZ NDP 2.07612
11 2ZMF CMP 2.1164
12 6F9Q NAD 2.20588
13 6ER9 NAP 2.39726
14 2Q28 TPP 2.39726
15 4OUC 5ID 2.39726
16 5JIC N7E 2.5641
17 5JIC ADP 2.5641
18 5F8F SFG 2.73973
19 1IYE PGU 2.73973
20 3TMK T5A 2.77778
21 1XTT U5P 2.77778
22 5OOH NAP 2.91262
23 5OOH 9ZZ 2.91262
24 2E5V FAD 3.08219
25 4KGD FAD 3.08219
26 4KGD TDP 3.08219
27 3UA1 08Y 3.08219
28 5KGS 6SR 3.08219
29 1M13 HYF 3.08219
30 3VZ3 SSN 3.08219
31 1WDN GLN 3.09735
32 3SFI 3SF 3.38983
33 2RGO FAD 3.42466
34 2RGH FAD 3.42466
35 5UN9 NHT 3.42466
36 5OC1 FAD 3.42466
37 3GF4 FAD 3.42466
38 4OM8 NAD 3.42466
39 2TPL HPP 3.42466
40 6AA8 NAD 3.42466
41 2ZB4 5OP 3.42466
42 2ZB4 NAP 3.42466
43 2QTR NXX 3.7037
44 5B48 TDN 3.76712
45 3V2U ATP 3.76712
46 4C3Y ANB 3.76712
47 4C3Y FAD 3.76712
48 2V7Y ADP 3.76712
49 4A62 ANP 3.76712
50 1ZPD DPX 3.76712
51 4OOE NDP 3.76712
52 5LAU AR6 3.84615
53 4CQM NAP 4.09836
54 5TS5 FAD 4.10959
55 1Q19 APC 4.10959
56 1J0X NAD 4.10959
57 1VPV PLM 4.10959
58 4PC3 GDP 4.10959
59 1MGP PLM 4.10959
60 2YCH ATP 4.10959
61 1U7T TDT 4.21456
62 1OZH HE3 4.24028
63 1XTP SAI 4.33071
64 3IGZ 2PG 4.45205
65 3IGZ 3PG 4.45205
66 1QHG ATP 4.45205
67 4YNU FAD 4.45205
68 5IRN ADP 4.45205
69 5FWJ MMK 4.45205
70 1QXO FMN 4.45205
71 5MWY YNU 4.45205
72 2AHR NAP 4.6332
73 4YDU ADP 4.64135
74 1VQ2 DDN 4.66321
75 1QD0 RR6 4.6875
76 1Q3Q ANP 4.79452
77 5ZUN 9JX 4.79452
78 5KJU 6TO 4.79452
79 4RDH AMP 4.86111
80 3RG9 NDP 5
81 3RG9 WRA 5
82 2C91 NAP 5.02959
83 4D79 ATP 5.07246
84 4U8P UDP 5.13699
85 4U8P FDA 5.13699
86 3IAE D7K 5.13699
87 2X7J TPP 5.13699
88 2UZ1 TPP 5.13699
89 4MO2 FDA 5.13699
90 4Z87 5GP 5.13699
91 2AOT SAH 5.13699
92 1DR1 NAP 5.29101
93 1DR1 HBI 5.29101
94 1IUP ALQ 5.31915
95 2IID PHE 5.47945
96 2IID FAD 5.47945
97 2VVM FAD 5.47945
98 3EFV NAD 5.47945
99 1VL8 NAP 5.61798
100 5J60 FAD 5.82192
101 4IP7 FBP 5.82192
102 3JUQ AKD 5.94595
103 3JUQ AJD 5.94595
104 5VL2 9EG 6.06061
105 1GQ2 NAP 6.16438
106 5ZYN FAD 6.16438
107 3RLF ANP 6.16438
108 4JGX PLM 6.20155
109 5B47 PYR 6.50685
110 5B47 TPP 6.50685
111 2YG3 FAD 6.50685
112 1OBV FMN 6.50888
113 4NCN GTP 6.56455
114 1M5W DXP 6.58436
115 3TYZ XHP 6.78571
116 2WTX UDP 6.84932
117 2WTX VDO 6.84932
118 2VK4 TPP 6.84932
119 4G17 0VN 6.84932
120 2FR6 CTN 6.84932
121 1SIV PSI 7.07071
122 1CZR FMN 7.10059
123 2RAB NAD 7.53425
124 5X40 ACP 7.53425
125 3PC3 P1T 7.87671
126 4YHQ G10 8.08081
127 4J4H NAI 8.49421
128 4J4H 1J1 8.49421
129 4JK3 NAD 8.49421
130 3GDN FAD 8.56164
131 3GDN HBX 8.56164
132 5EHZ 5NZ 8.56164
133 1AKV FMN 8.84354
134 4GIM PSU 8.90411
135 1T3Q FAD 8.92857
136 3AD8 NAD 9.09091
137 2O4N TPV 9.09091
138 1EWF PC1 9.24658
139 5EIB GTP 9.46746
140 1N62 FAD 9.72222
141 5FAL SKT 9.93151
142 5FAL COA 9.93151
143 2PBD ATP 11.5108
144 1REO FAD 12.3288
145 5ABH YWN 13.6986
146 2CHN NGT 13.6986
147 5ABF XRJ 13.6986
148 3A28 NAD 14.3411
149 4J5R A1R 14.3836
150 1D4D FAD 14.3836
151 1L3I SAH 15.1042
152 2D0O ADP 16
153 5X3D 7XL 18.125
154 5M7S NHT 26.7123
155 4PTN GXV 40.7534
Pocket No.: 3; Query (leader) PDB : 3I7S; Ligand: PYR; Similar sites found with APoc: 14
This union binding pocket(no: 3) in the query (biounit: 3i7s.bio2) has 9 residues
No: Leader PDB Ligand Sequence Similarity
1 2WZF BGC 1.36986
2 5AHM IMP 2.39726
3 6A3J NAI 2.39726
4 3Q9T FAY 2.73973
5 4PZ2 NAD 3.08219
6 2AE2 NAP 4.23077
7 2AE2 PTO 4.23077
8 4NG2 OHN 4.42478
9 2C6Q NDP 4.79452
10 5GWT NAD 5.03597
11 3E85 BSU 5.06329
12 6F7L FAD 7.19178
13 4K79 GAL A2G 8.63636
14 4U0W 16G 10.1626
Pocket No.: 4; Query (leader) PDB : 3I7S; Ligand: PYR; 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: 3i7s.bio2) has 9 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 5; Query (leader) PDB : 3I7S; Ligand: PYR; Similar sites found with APoc: 16
This union binding pocket(no: 5) in the query (biounit: 3i7s.bio2) has 10 residues
No: Leader PDB Ligand Sequence Similarity
1 5G3U ITW 2.05479
2 4JD3 PLM 2.73973
3 1PJS NAD 3.08219
4 1A8R GTP 3.16742
5 6DEN FAD 3.42466
6 6DEN G8A 3.42466
7 6DEN TP9 3.42466
8 3MN5 ATP 3.76712
9 4MO2 FAD 5.13699
10 1H74 ILE 5.40541
11 5XJ8 NKO 6.46766
12 2VZZ SCA 6.88073
13 1TQ4 GDP 7.53425
14 4IXH IMP 7.87671
15 5CSD ACD 8.1761
16 5EOB 5QQ 8.90411
Pocket No.: 6; Query (leader) PDB : 3I7S; Ligand: PYR; 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: 3i7s.bio2) has 10 residues
No: Leader PDB Ligand Sequence Similarity
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