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Receptor
PDB id Resolution Class Description Source Keywords
3BY9 1.7 Å EC: 2.7.13.3 CRYSTAL STRUCTURE OF THE V. CHOLERAE HISTIDINE KINASE DCTB S DOMAIN VIBRIO CHOLERAE HISTIDINE KINASE SENSOR DOMAIN PHOSPHOPROTEIN TRANSFERASECOMPONENT REGULATORY SYSTEM
Ref.: CRYSTAL STRUCTURES OF C4-DICARBOXYLATE LIGAND COMPL SENSOR DOMAINS OF HISTIDINE KINASES DCUS AND DCTB. J.BIOL.CHEM. V. 283 30256 2008
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
CA A:1;
A:2;
Part of Protein;
Part of Protein;
none;
none;
submit data
40.078 Ca [Ca+2...
SIN A:287;
B:288;
Valid;
Valid;
none;
none;
submit data
118.088 C4 H6 O4 C(CC(...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
3BY9 1.7 Å EC: 2.7.13.3 CRYSTAL STRUCTURE OF THE V. CHOLERAE HISTIDINE KINASE DCTB S DOMAIN VIBRIO CHOLERAE HISTIDINE KINASE SENSOR DOMAIN PHOSPHOPROTEIN TRANSFERASECOMPONENT REGULATORY SYSTEM
Ref.: CRYSTAL STRUCTURES OF C4-DICARBOXYLATE LIGAND COMPL SENSOR DOMAINS OF HISTIDINE KINASES DCUS AND DCTB. J.BIOL.CHEM. V. 283 30256 2008
Members (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 18 families.
1 3BY9 - SIN C4 H6 O4 C(CC(=O)O)....
70% Homology Family (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 18 families.
1 3BY9 - SIN C4 H6 O4 C(CC(=O)O)....
50% Homology Family (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 15 families.
1 3BY9 - SIN C4 H6 O4 C(CC(=O)O)....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: SIN; Similar ligands found: 17
No: Ligand ECFP6 Tc MDL keys Tc
1 SIN 1 1
2 3OH 0.6 0.65
3 SHF 0.588235 0.684211
4 BUA 0.5625 0.611111
5 SLP 0.5625 0.6
6 0L1 0.5625 0.833333
7 GUA 0.5625 0.882353
8 AKG 0.526316 0.833333
9 PML 0.5 0.789474
10 MLA 0.5 0.722222
11 2IT 0.5 0.625
12 SSN 0.473684 0.866667
13 AZ1 0.473684 0.75
14 OKG 0.454545 0.7
15 TCE 0.45 0.625
16 SHO 0.428571 0.619048
17 9J3 0.416667 0.608696
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 3BY9; Ligand: SIN; Similar sites found with APoc: 258
This union binding pocket(no: 1) in the query (biounit: 3by9.bio2) has 12 residues
No: Leader PDB Ligand Sequence Similarity
1 3UIE ANP None
2 5APK 76E None
3 4BNU 9KQ None
4 2AMT GPP None
5 4M20 COA None
6 1T0A FPP None
7 2WLG SOP None
8 5AYV KPL 1.15385
9 3OID NDP 1.16279
10 1DQS NAD 1.53846
11 4G1V FAD 1.92308
12 3QV1 NAD 1.92308
13 3EKK GS2 1.92308
14 2CSN CKI 1.92308
15 3KAL HGS 1.92308
16 1J78 OLA 1.92308
17 2BEK ATP 1.94553
18 5X0J AMP 2.06612
19 3RK1 ATP 2.1097
20 4JB1 NAP 2.30769
21 4JB1 FAD 2.30769
22 1N62 MCN 2.30769
23 3CGB FAD 2.30769
24 1GQY ACP 2.30769
25 4ZXF 4S7 2.30769
26 1N62 FAD 2.30769
27 2OM2 GDP 2.30769
28 5G1N PAL 2.30769
29 4A59 AMP 2.30769
30 1TAD ALF 2.30769
31 1TAD GDP 2.30769
32 5J1J ANP 2.30769
33 3BF1 ADP 2.40964
34 1LK7 DER 2.62009
35 2CHG ANP 2.65487
36 1QF5 RPL 2.69231
37 1QF5 GDP 2.69231
38 4B4D FAD 2.69231
39 6FAA ADP 2.69231
40 1A99 PUT 2.69231
41 1SM4 FAD 2.69231
42 1FND FAD 2.69231
43 1FND A2P 2.69231
44 3TTM PUT 2.69231
45 4LY9 S6P 2.69231
46 3VO1 FAD 2.69231
47 1IYE PGU 2.69231
48 2GKS ADP 2.69231
49 4KVA GTP 2.69231
50 4IOK XPO 2.69231
51 6H3O FAD 2.69231
52 3TDV GDP 2.69231
53 4LZJ 22H 2.69231
54 2VOS ADP 2.69231
55 1GAW FAD 2.69231
56 2GMH UQ5 2.69231
57 4IY7 KOU 2.69231
58 1UJ2 ADP 2.77778
59 1UJ2 C5P 2.77778
60 4MUV PCG 2.8169
61 4U9U FAD 2.84698
62 2OFW ADX 2.88462
63 3B9A NAG NAG NAG NAG NAG NAG 3.07692
64 5Y1G AKB 3.07692
65 1Q9I FAD 3.07692
66 1Q9I TEO 3.07692
67 2ZXI FAD 3.07692
68 2CDU FAD 3.07692
69 4HDH ATP 3.07692
70 4DQL FAD 3.07692
71 2Z23 LYS LYS LYS 3.07692
72 5OGX FAD 3.07692
73 4DQL NAP 3.07692
74 3BFV ADP 3.07692
75 4RGQ NDP 3.07692
76 6CLV 6MB 3.07692
77 4CCW VKC 3.07692
78 3I6I NDP 3.07692
79 6ACS CIT 3.10078
80 2H92 C5P 3.19635
81 2Y7P SAL 3.21101
82 2PEZ DAT 3.35196
83 5JVB 2PO 3.46154
84 2JLR ANP 3.46154
85 2VNI A2P 3.46154
86 2VNI FAD 3.46154
87 2WHX ADP 3.46154
88 2RC5 FAD 3.46154
89 2WOJ ADP ALF 3.46154
90 3NTD FAD 3.46154
91 1P0F NAP 3.46154
92 5T9F NAP 3.46154
93 5T9F TYR 3.46154
94 3B4Y F42 3.46154
95 1TLL FAD 3.46154
96 1NZY BCA 3.46154
97 1W5T ANP 3.46154
98 5D85 P1T 3.46154
99 3JQQ FAD 3.48101
100 5AVF TAU 3.50195
101 2YC5 6BC 3.50877
102 2V68 CAP 3.57143
103 2FXV 5GP 3.60825
104 1IWE IMP 3.84615
105 1J0D 5PA 3.84615
106 1PVN MZP 3.84615
107 2BSA NAP 3.84615
108 2BSA FAD 3.84615
109 1RE8 BD2 3.84615
110 5O4J SAH 3.84615
111 3KCC CMP 3.84615
112 6ER9 FAD 3.84615
113 5O4J 9KH 3.84615
114 3ZL8 ADP 3.84615
115 5O4J PJL 3.84615
116 3RC1 NAP 3.84615
117 1Q19 APC 3.84615
118 3S7D SAH 3.84615
119 4RZB NFQ 3.84615
120 5ZBC FAD 3.84615
121 5DEX 5E0 3.84615
122 1Q3Q ANP 3.84615
123 3OEN GLU 3.84615
124 2HF9 GSP 3.9823
125 4X7G 3Y8 3.98406
126 4QM7 GTP 4.09357
127 4XVU ATP 4.14747
128 4HUT ATP 4.18848
129 5O2J 2PO 4.23077
130 1E2K TMC 4.23077
131 5FB3 NDP 4.23077
132 5YLY FAD 4.23077
133 4FWE FAD 4.23077
134 3PFG SAM 4.23077
135 3PFG TLO 4.23077
136 4OJ8 AKG 4.23077
137 4OJ8 2TQ 4.23077
138 1UOU CMU 4.23077
139 1DUV PSQ 4.23077
140 5YSE BGC BGC BGC GLC 4.23077
141 1CS4 GSP 4.24528
142 2BOY BHO 4.33071
143 1Y63 ADP 4.34783
144 3R5W F42 4.46429
145 4MO4 ACP 4.58221
146 4WZA ADP 4.61538
147 3ZQ6 ADP ALF 4.61538
148 4WZA ACP 4.61538
149 2X7I CIT 4.61538
150 4QYS PLP SEP 4.61538
151 4Y30 SAH 4.61538
152 4CJX NAP 4.61538
153 2C49 ANP 4.61538
154 5O0X FAD 4.61538
155 6F5Z SAH 4.91803
156 3KO0 TFP 4.9505
157 1VEM GLC GLC 5
158 1Z0N BCD 5.20833
159 5T2U NAP 5.24194
160 3IP8 B85 5.24194
161 1TQP ATP 5.38462
162 3UZO GLU 5.38462
163 3VMF GTP 5.38462
164 3DVA TPW 5.38462
165 1M7G ADX 5.6872
166 1M7G ADP 5.6872
167 2EIX FAD 5.76132
168 5LV1 78T 5.76923
169 4ZCW 4NG 5.76923
170 4Q9N NAI 5.76923
171 4Y1B NAP 5.76923
172 3EXH TPP 5.76923
173 5ODQ 9SB 5.76923
174 2B4Q NAP 5.7971
175 3OZV FAD 6.15385
176 3OZV ECN 6.15385
177 5GXU FAD 6.15385
178 5LXT GDP 6.29371
179 5LXT 7AK 6.29371
180 1H65 GDP 6.53846
181 3OTH TYD 6.53846
182 3FV1 DYH 6.64062
183 3IAE D7K 6.92308
184 2OG2 MLI 6.92308
185 5HV7 RBL 6.92308
186 3B9Q MLI 6.92308
187 2BLE 5GP 6.92308
188 5X20 NAD 6.92308
189 2VAT COA 6.92308
190 5L3R GCP 6.92308
191 4AP9 1PS 6.96517
192 2VOH CIT 7.00637
193 1KOL NAD 7.28643
194 4YRY FAD 7.30769
195 1RJ9 GCP 7.30769
196 5L3S GNP 7.30769
197 1RM6 FAD 7.45342
198 4H4D 10E 7.69231
199 1QS0 TDP 7.69231
200 3KLJ FAD 8.07692
201 2R5V HHH 8.07692
202 5FPE 3TR 8.07692
203 3R7F CP 8.07692
204 5DXV NAP 8.33333
205 4KM2 TOP 8.37989
206 5LTJ ADP 8.46154
207 1RRC ADP 8.46154
208 2UYT ADP 8.46154
209 2UYT LRH 8.46154
210 3WXL ADP 8.46154
211 2IO8 ADP 8.46154
212 3CRZ FAD 8.56031
213 3R5Y F42 8.84354
214 1OTH PAO 8.84615
215 3AJ4 SEP 8.92857
216 2ZGY GDP 9.0625
217 5H7K GDP 9.23077
218 2ZYI STE 9.23077
219 5H5J FAD 9.27835
220 2NPX FAD 9.61539
221 5GWT NAD 9.71223
222 3SJ7 NDP 9.92064
223 2WK2 SN5 SN5 10
224 2WK2 SN5 SN5 NGT 10
225 5YJF 8WO 10
226 4BQS ADP 10.2273
227 1YTM ATP 10.3846
228 6CUZ FEV 10.3846
229 3A4M ADP 10.3846
230 3GWN FAD 10.5263
231 5CMK GLU 10.8108
232 4A62 ANP 11.1538
233 5U32 GDP 11.4407
234 4WOH 4NP 11.4458
235 4L9Z COA 11.5044
236 3N29 GOL 11.5385
237 1P9B HDA 11.9231
238 5XQL C2E 11.9231
239 5Y6N ADP 11.9231
240 4DV8 0LX 11.9231
241 1QM5 GLC GLC GLC PO4 SGC GLC 12.3077
242 1WA5 GTP 12.5
243 3WYG GTP 12.6374
244 4WQM FAD 13.0769
245 4CVN ADP 13.6126
246 2AWN ADP 13.8462
247 3IA4 NDP 14.1975
248 1EWY FAD 14.2857
249 3WXM GTP 15
250 3E5A VX6 15.9091
251 3IIJ ADP 16.1111
252 1QS8 IVA VAL VAL STA ALA STA 16.1538
253 4OOP DUP 18.0723
254 3ZS9 ADP ALF 18.4211
255 1M2O GNP 18.4615
256 1SQ5 ADP 20.7692
257 2XAU ADP 21.5385
258 3MHP FAD 30.7692
Pocket No.: 2; Query (leader) PDB : 3BY9; Ligand: SIN; Similar sites found with APoc: 139
This union binding pocket(no: 2) in the query (biounit: 3by9.bio1) has 13 residues
No: Leader PDB Ligand Sequence Similarity
1 1A8R GTP None
2 4CNK FAD 1.15385
3 5VYR B62 1.15385
4 5VYR GMP 1.15385
5 4REL KMP 1.53846
6 5EYG NAP 1.53846
7 1EBG PAH 1.53846
8 2I0G I0G 1.55642
9 2X1L ADN 1.92308
10 4XQC 13D 1.92308
11 4XQC NAD 1.92308
12 1Z0S ATP 1.92308
13 2CND FAD 1.92308
14 3RHZ UDP 1.92308
15 2HIM ASN 1.95531
16 3CGD NAD 2.30769
17 3CGD FAD 2.30769
18 3CGD COA 2.30769
19 1QH5 GSH 2.30769
20 2PTZ PAH 2.30769
21 3WLE NAD 2.30769
22 4B0T ADP 2.30769
23 5W75 SUC 2.30769
24 4XO8 KGM 2.53165
25 1QFY NAP 2.69231
26 1QFY FAD 2.69231
27 5YJI SAH 2.69231
28 1EGD FAD 2.69231
29 1Q6O LG6 2.77778
30 1O44 852 2.77778
31 1SMR PIV HIS PRO PHE HIS LPL TYR TYR SER 3.07692
32 2CFD R4A 3.07692
33 4GA6 AMP 3.07692
34 5BVE 4VG 3.07692
35 2R5T ANP 3.07692
36 1E3I CXF 3.07692
37 3WG6 NDP 3.07692
38 3NRZ HPA 3.07692
39 1D2E GDP 3.07692
40 3IID APR 3.31754
41 4RHE FMN 3.34928
42 5VN0 FAD 3.46154
43 5W3K 9TY 3.46154
44 2D8L UCD 3.46154
45 1RKX NAD 3.46154
46 5W3K NDP 3.46154
47 3TWO NDP 3.46154
48 1JGT APC 3.46154
49 1JGT CMA 3.46154
50 2C6Q IMP 3.46154
51 2E5A LAQ 3.46154
52 5H81 NAP 3.46154
53 3AXX CBI 3.46154
54 5EPO TUD 3.46154
55 1FIQ SAL 3.65297
56 1FIQ MTE 3.65297
57 5FI3 NAP 3.84615
58 3BOF HCS 3.84615
59 1EZ0 NAP 3.84615
60 1Q8A HCS 3.84615
61 1B7H LYS NLE LYS 3.84615
62 1P72 ADP 3.84615
63 5WKC TP9 3.84615
64 5WKC AUJ 3.84615
65 3CTL S6P 3.8961
66 3FPZ AHZ 3.98773
67 5E5U MLT 4.0201
68 1JNR FAD 4.23077
69 4KQW NAP 4.23077
70 2F2H XTG 4.23077
71 2QE4 JJ3 4.43548
72 1IM8 SAI 4.5082
73 3EYA FAD 4.61538
74 4OOE NDP 4.61538
75 4OOE FOM 4.61538
76 5ME4 HP4 4.61538
77 5GVL PLG 4.61538
78 5GVL GI8 4.61538
79 1OLS TDP 4.61538
80 3GNE FLC 4.7619
81 3N0S ACO 5
82 4MP8 MLI 5
83 4MP8 NAD 5
84 4HBM 0Y7 5
85 4UTG ANP 5
86 1SR7 MOF 5.01931
87 3W9K MYR 5.03597
88 2CJF RP4 5.09554
89 2YCH ATP 5.38462
90 3A06 NDP 5.38462
91 1HYH NAD 5.38462
92 2GVC FAD 5.38462
93 4WK1 2BA 5.42636
94 3WBF API 5.57377
95 5OVX AY5 5.57377
96 5VW2 NAP 5.76923
97 5VW2 FDA 5.76923
98 1OJ7 NZQ 5.76923
99 4J56 FAD 5.76923
100 5JKG 6LF 5.76923
101 1F06 2NP 5.76923
102 1F06 NDP 5.76923
103 3RYC GTP 5.76923
104 1FUR MLT 6.15385
105 1WVG APR 6.15385
106 5E4R NAP 6.15385
107 4CBU ATP 6.15385
108 3H86 AP5 6.25
109 5VHC BEF ADP 6.53846
110 3W2E NAD 6.53846
111 3W2E FAD 6.53846
112 4XDZ NDP 6.99708
113 1GT4 UNA 7.54717
114 5B48 TDN 7.69231
115 2BHZ MAL 7.69231
116 1MEX RAC 7.90698
117 5XKT GNP 8
118 1OS1 ATP 8.07692
119 4A0S NAP 8.46154
120 4P87 4NP 9.23077
121 1Z3C SA8 9.61539
122 4H2D FMN 9.69697
123 5GWT SIN 9.71223
124 5YJF SAH 10
125 4BQS K2Q 10.2273
126 4FAJ LEU VAL THR LEU VAL PHE VAL 10.3846
127 4UXH T5A 10.8696
128 1T36 ORN 11.1538
129 3FPF MTA 11.745
130 3FPF TNA 11.745
131 3OII SAH 12.253
132 3SLS 77D 12.3077
133 4LNU GTP 15.3846
134 1FHX 4IP 16.2791
135 2V3V MGD 16.5385
136 1LN1 DLP 18.6916
137 3RFV NAI 20
138 4NE2 SH2 20.3846
139 4NE2 ADP 20.3846
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