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Receptor
PDB id Resolution Class Description Source Keywords
5W10 2.15 Å EC: 7.-.-.- LCD1 GAF DOMAIN IN COMPLEX WITH CAMP LIGAND LEPTOSPIRA INTERROGANS SEROGROUP ICTEROHAEMORRHAGIAE SEROVAR COPENHAGENI (STRAIN FIOCRUZ L1-ORGANISM_TAXID: 267671 GAF DOMAIN CAMP BINDING DOMAIN EFFECTOR DOMAIN REGULATES ACTIVITY OF THE GGDEF DOMAIN HYDROLASE
Ref.: STRUCTURAL AND ENZYMATIC CHARACTERIZATION OF A CAMP-DEPENDENT DIGUANYLATE CYCLASE FROM PATHOGENIC LEPTOSPIRA SPECIES. J. MOL. BIOL. V. 429 2337 2017
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
CMP B:201;
A:201;
C:201;
D:201;
Valid;
Valid;
Valid;
Valid;
none;
none;
none;
none;
Kd = 0.24 uM
329.206 C10 H12 N5 O6 P c1nc(...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
5W10 2.15 Å EC: 7.-.-.- LCD1 GAF DOMAIN IN COMPLEX WITH CAMP LIGAND LEPTOSPIRA INTERROGANS SEROGROUP ICTEROHAEMORRHAGIAE SEROVAR COPENHAGENI (STRAIN FIOCRUZ L1-ORGANISM_TAXID: 267671 GAF DOMAIN CAMP BINDING DOMAIN EFFECTOR DOMAIN REGULATES ACTIVITY OF THE GGDEF DOMAIN HYDROLASE
Ref.: STRUCTURAL AND ENZYMATIC CHARACTERIZATION OF A CAMP-DEPENDENT DIGUANYLATE CYCLASE FROM PATHOGENIC LEPTOSPIRA SPECIES. J. MOL. BIOL. V. 429 2337 2017
Members (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 293 families.
1 5W10 Kd = 0.24 uM CMP C10 H12 N5 O6 P c1nc(c2c(n....
70% Homology Family (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 250 families.
1 5W10 Kd = 0.24 uM CMP C10 H12 N5 O6 P c1nc(c2c(n....
50% Homology Family (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 204 families.
1 5W10 Kd = 0.24 uM CMP C10 H12 N5 O6 P c1nc(c2c(n....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: CMP; Similar ligands found: 93
No: Ligand ECFP6 Tc MDL keys Tc
1 2BA 1 0.984848
2 CMP 1 1
3 RP1 0.757143 0.928571
4 SP1 0.757143 0.928571
5 1YD 0.727273 0.902778
6 4BW 0.727273 0.902778
7 1SY 0.653061 0.902778
8 1OR 0.635294 0.807692
9 4UR 0.626263 0.902778
10 7CH 0.580247 0.984615
11 6SX 0.573171 0.953846
12 6SZ 0.559524 0.984848
13 N6R 0.535354 0.914286
14 N6S 0.535354 0.914286
15 PCG 0.534091 0.888889
16 35G 0.534091 0.888889
17 C2E 0.534091 0.902778
18 1YC 0.53 0.875
19 Y3J 0.506667 0.753623
20 XYA 0.5 0.826087
21 5CD 0.5 0.811594
22 ACK 0.5 0.897059
23 RAB 0.5 0.826087
24 ADN 0.5 0.826087
25 6SW 0.494382 0.9
26 5AD 0.493151 0.776119
27 5N5 0.486842 0.8
28 75G 0.483146 0.890411
29 A4D 0.480519 0.8
30 M2T 0.475 0.736842
31 MTA 0.469136 0.777778
32 CC5 0.466667 0.850746
33 EP4 0.4625 0.756757
34 DTA 0.45679 0.816901
35 QQX 0.452381 0.835616
36 LMS 0.447059 0.7875
37 AMP 0.447059 0.927536
38 QQY 0.447059 0.847222
39 A 0.447059 0.927536
40 3DH 0.440476 0.777778
41 3AM 0.435294 0.913043
42 A2D 0.431818 0.928571
43 J7C 0.431818 0.75
44 ABM 0.431818 0.901408
45 ZAS 0.430233 0.77027
46 7D7 0.428571 0.771429
47 S4M 0.426966 0.666667
48 SRA 0.425287 0.876712
49 6RE 0.425287 0.74026
50 3AD 0.425 0.838235
51 2AM 0.423529 0.9
52 BA3 0.422222 0.928571
53 A12 0.422222 0.864865
54 AP2 0.422222 0.864865
55 MAO 0.422222 0.740741
56 DSH 0.420455 0.727273
57 NEC 0.420455 0.726027
58 AOC 0.420455 0.802817
59 A3G 0.420455 0.780822
60 SFG 0.419355 0.753425
61 6JR 0.419048 0.927536
62 ADP 0.417582 0.901408
63 AP5 0.417582 0.928571
64 5AS 0.417582 0.741176
65 B4P 0.417582 0.928571
66 A3N 0.41573 0.767123
67 APC 0.414894 0.864865
68 AN2 0.413043 0.888889
69 SON 0.413043 0.864865
70 AT4 0.413043 0.864865
71 EEM 0.412371 0.691358
72 GJV 0.411111 0.730769
73 GGZ 0.41 0.78481
74 OVE 0.409091 0.863014
75 M33 0.408602 0.888889
76 ADX 0.408602 0.810127
77 AU1 0.408602 0.876712
78 CA0 0.408602 0.876712
79 A3P 0.406593 0.927536
80 5X8 0.404255 0.767123
81 ATP 0.404255 0.901408
82 ACP 0.404255 0.876712
83 HEJ 0.404255 0.901408
84 50T 0.404255 0.888889
85 ADP VO4 0.40404 0.888889
86 VO4 ADP 0.40404 0.888889
87 SAM 0.402062 0.691358
88 0UM 0.401961 0.7
89 AR6 0.4 0.901408
90 AQP 0.4 0.901408
91 5FA 0.4 0.901408
92 APR 0.4 0.901408
93 PRX 0.4 0.876712
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 5W10; Ligand: CMP; Similar sites found with APoc: 217
This union binding pocket(no: 1) in the query (biounit: 5w10.bio1) has 21 residues
No: Leader PDB Ligand Sequence Similarity
1 4K55 H6P None
2 4USI AKG None
3 4X8O AP5 None
4 5EZU MYR None
5 3BU1 HSM None
6 2VQ5 HBA None
7 4PYA 2X3 None
8 1N5S ADL None
9 4Z28 BTN None
10 2DT9 THR None
11 6FA4 D1W None
12 3QXV MTX None
13 5ISY NAD 1.53846
14 2OVD DAO 1.64835
15 2D6M LBT 1.88679
16 5F6U 5VK 1.91083
17 6ACS CIT 2.05128
18 1M1B SPV 2.05128
19 1GQG DCD 2.05128
20 2P7Q GG6 2.25564
21 4INI AMP 2.30769
22 5IXG OTP 2.36686
23 3BRN SRO 2.54777
24 3BF8 MLA 2.5641
25 5HV7 RBL 2.5641
26 1OFL NGK GCD 2.5641
27 6CED EYA 2.5641
28 4RDL FUC GAL NDG FUC 2.5641
29 4YGF AZM 2.5641
30 5J75 6GQ 2.5641
31 3KYF 5GP 5GP 3.07692
32 2NSX IFM 3.07692
33 4XFR CIT 3.07692
34 5DQ8 FLF 3.07692
35 4FBL SPD 3.07692
36 5ZI9 FLC 3.07692
37 1DMY AZM 3.07692
38 4ITH RCM 3.07692
39 3BOF HCS 3.07692
40 4H6B 10X 3.07692
41 1Q8A HCS 3.07692
42 1Y9Q MED 3.125
43 5TZO 7V7 3.19149
44 3AB4 THR 3.37079
45 5LUN OGA 3.58974
46 5OC1 ANN 3.58974
47 5NXX 3Q7 3.58974
48 5HA0 LTD 3.58974
49 5LUN ARG 3.58974
50 4QAC KK3 3.58974
51 5T8U LPA 3.58974
52 3QP6 HL6 3.58974
53 4ZUL UN1 3.58974
54 3G0I VPR 3.58974
55 1T27 PCW 3.58974
56 2IOY RIP 3.58974
57 3T4L ZEA 3.58974
58 2IXC TRH 3.58974
59 4JGP PYR 3.58974
60 6GWR FEW 3.58974
61 1J3R 6PG 3.68421
62 2GC0 PAN 3.7234
63 1MDC PLM 3.78788
64 3QRC SCR 3.82166
65 5JJ2 MLI 4.10256
66 4BR5 ANP 4.10256
67 5A5W GUO 4.10256
68 3E8N ATP 4.10256
69 3E8N VRA 4.10256
70 6HDT BTN 4.10256
71 1OIK AKG 4.10256
72 1QKQ MAN 4.22535
73 3NV3 GAL NAG MAN 4.34783
74 3E85 BSU 4.43038
75 5ACM MBT 4.5045
76 1QY1 PRZ 4.5977
77 2YMZ LAT 4.61538
78 1Z03 OCH 4.61538
79 3ZJX BOG 4.61538
80 5W4W 9WG 4.61538
81 5IN4 GDP 4.61538
82 1EK6 NAI 4.61538
83 1EK6 UPG 4.61538
84 4KBA 1QM 4.61538
85 4U0I 0LI 4.61538
86 4MSG 2C6 4.61538
87 1WTC ACP 4.61538
88 5W75 SUC 4.61538
89 6F5W KG1 4.61538
90 1ZGS XMM 4.61538
91 1I82 BGC BGC 4.7619
92 4WVW SLT 4.86111
93 4NG2 OHN 4.8913
94 3WG3 A2G GAL NAG FUC 5.05618
95 1DZK PRZ 5.09554
96 2C5A GDC 5.12821
97 2C5A NAD 5.12821
98 5D9G GLU ASN LEU TYR PHE GLN 5.12821
99 1VJY 460 5.12821
100 1S7G APR 5.12821
101 6GNO XDI 5.18518
102 5OCG 9R5 5.29101
103 1P0Z FLC 5.34351
104 1KJ1 MAN 5.50459
105 6A1G 9OL 5.55556
106 6BFH KAN 5.61798
107 5YJS SAL 5.64103
108 5W1E PHB 5.64103
109 4G31 0WH 5.64103
110 5MJA 7O3 5.64103
111 5G1N PAL 5.64103
112 4CQE CQE 5.7554
113 3KO0 TFP 5.94059
114 3ZXE PGZ 6.01504
115 5KOD IAC 6.15385
116 2GQS C2R 6.15385
117 6DW2 HD4 6.15385
118 4YDU ADP 6.15385
119 3VP6 HLD 6.15385
120 3T3Z 9PL 6.15385
121 5FBN 5WF 6.15385
122 5AOV GLV 6.15385
123 4LED XXR 6.15385
124 2GJ5 VD3 6.17284
125 3VV1 GAL FUC 6.25
126 1Y0G 8PP 6.28272
127 4K7O EKZ 6.54762
128 4RYV ZEA 6.66667
129 3VSV XYP 6.66667
130 1ZZ7 S0H 6.66667
131 5XVG 8FX 6.66667
132 4F4P 0SB 6.66667
133 5H2U 1N1 6.74157
134 5FIT AP2 6.80272
135 5NFB 8VT 6.81818
136 4X5S AZM 7.17949
137 5HCY 60D 7.17949
138 1ZTH ADP 7.17949
139 1F5F DHT 7.17949
140 2QL9 CIT 7.2165
141 5GLT BGC GAL NAG GAL 7.39437
142 2YNE YNE 7.69231
143 2YNE NHW 7.69231
144 6BR9 PGV 7.69231
145 4YJK URA 7.69231
146 1UNB PN1 7.69231
147 1KDK DHT 7.9096
148 4IAW LIZ 7.97872
149 5IXH OTP 8.07453
150 5KJW 53C 8.20513
151 5LXB 7A9 8.20513
152 5BVE 4VG 8.20513
153 3OYW TDG 8.20895
154 5DYO FLU 8.49057
155 5NLD LBT 8.63309
156 1LSH PLD 8.71795
157 5C9J DAO 8.71795
158 3G5D 1N1 8.71795
159 1DRJ RIP 8.71795
160 1C1L GAL BGC 8.75912
161 1ZM1 BGC BGC BGC 9.23077
162 6F9G PUT 9.23077
163 1SLT NDG GAL 9.70149
164 4OIT MAN 9.73451
165 3A16 PXO 9.74359
166 4LIT AKG 9.74359
167 4G7A AZM 9.74359
168 5WL1 D3D 9.74359
169 5WL1 CUY 9.74359
170 2OFV 242 9.74359
171 4WO4 JLS 9.74359
172 2QRY TPS 9.74359
173 2YKL NLD 9.90566
174 5HWV MBN 10
175 2G30 ALA ALA PHE 10.2564
176 4RD0 GDP 10.2564
177 5DCH 1YO 10.2564
178 1Q9I FAD 10.2564
179 1Q9I TEO 10.2564
180 2XKO AKG 10.3604
181 2XHK AKG 10.3604
182 4JNJ BTN 10.4348
183 3LA3 2FT 10.7692
184 2RDE C2E 10.7692
185 3GL0 HXX 10.7692
186 2YKX AKG 10.7692
187 1ZNY GDP 11.1111
188 5TVM PUT 11.2821
189 6GK6 MYR 11.7949
190 3MBI HSX 11.7949
191 4Y24 TD2 12.3377
192 5H9P TD2 12.6582
193 3IWD M2T 13.2353
194 1VRP ADP 13.3333
195 4LRJ ANP 14.2012
196 4F7E 0SH 14.2857
197 4N70 2HX 14.359
198 2DUR MAN MAN 14.359
199 3ANY 2A3 14.359
200 4RF7 ARG 14.8718
201 1T0S BML 15.1163
202 1YFS ALA 16.4103
203 2ET1 GLV 16.4103
204 4WOE ADP 16.4103
205 5H9Q TD2 16.7742
206 2O3Z AI7 17.9487
207 3MMH SME 17.9641
208 2ADA HPR 18.4615
209 2TPS TPS 18.9744
210 5A89 FMN 19.8718
211 5A89 ADP 19.8718
212 3A76 SPD 20.4545
213 3L5R 47X 21.3115
214 1A78 TDG 27.6119
215 4MN7 SME 29.5302
216 1YKD CMP 37.9487
217 2ZMF CMP 39.1534
Pocket No.: 2; Query (leader) PDB : 5W10; Ligand: CMP; Similar sites found with APoc: 38
This union binding pocket(no: 2) in the query (biounit: 5w10.bio1) has 21 residues
No: Leader PDB Ligand Sequence Similarity
1 5T2Z 017 None
2 1OS7 AKG 1.53846
3 2YGO PCF 2.12766
4 1C3V PDC 2.5641
5 1Y7P RIP 3.07692
6 3WV6 GAL BGC 3.07692
7 5EW9 5VC 3.07692
8 2GMH UQ5 3.07692
9 3HQP OXL 3.07692
10 1LOJ URI 3.44828
11 1LOJ U 3.44828
12 2YAJ 4HP 3.48837
13 3CL5 SIO 3.58974
14 4AG8 AXI 3.58974
15 5T96 79J 3.58974
16 3TTI KBI 4.10256
17 4XMF HSM 4.34783
18 2DC1 CIT 4.61538
19 1SBR VIB 4.61538
20 1WUB OTP 5.12821
21 3WUD GLC GAL 5.14706
22 3RMK BML 5.64103
23 4L3L 5FI 6.15385
24 5KEW 6SB 6.25
25 3RWP ABQ 7.17949
26 5U98 1KX 8.08081
27 1J0D 5PA 8.20513
28 5N53 8NB 9.23077
29 5OFW 9TW 9.23077
30 3SAO DBH 9.375
31 4OKD GLC GLC GLC 9.74359
32 2UXR ICT 11.2821
33 5GQX GLC GLC GLC GLC 13.8462
34 3ACL 3F1 13.8462
35 4B2Z P5S 14.359
36 1RM0 NAI 16.4103
37 5N0L ILE 18.8679
38 2FNU PMP UD1 21.0256
Pocket No.: 3; Query (leader) PDB : 5W10; Ligand: CMP; Similar sites found with APoc: 22
This union binding pocket(no: 3) in the query (biounit: 5w10.bio2) has 21 residues
No: Leader PDB Ligand Sequence Similarity
1 6D61 4AA 1.02564
2 5Z2F PDC 3.01887
3 5HES 032 3.58974
4 3QP8 HL0 3.80435
5 1ULE GLA GAL NAG 4
6 4RT1 C2E 4.46429
7 1SB8 UD2 4.61538
8 4XV1 904 5.47945
9 6GZD LCI 5.64103
10 3WUC GLC GAL 5.83942
11 6FOF LAT 6.12245
12 3VRY B43 6.15385
13 4S1D 41M 6.66667
14 6GIN IR2 6.66667
15 6H3O FAD 6.66667
16 4U9W COA 6.66667
17 1USF NAP 6.74157
18 4KYS VIB 8.20513
19 2EAE LBT 9.23077
20 5DG2 GAL GLC 9.62963
21 4NPT 017 10.101
22 1IS3 LAT 12.5926
Pocket No.: 4; Query (leader) PDB : 5W10; Ligand: CMP; Similar sites found with APoc: 12
This union binding pocket(no: 4) in the query (biounit: 5w10.bio2) has 21 residues
No: Leader PDB Ligand Sequence Similarity
1 1GPM AMP 3.07692
2 1N7G GDR 4.61538
3 3T50 FMN 4.6875
4 3GC8 B45 6.15385
5 5UR1 YY9 6.15385
6 5Y4R C2E 7.58621
7 4ONA UW1 8.71795
8 5N2D 8J8 9.72222
9 3KFF ZBT 11.1111
10 3KFF XBT 11.1111
11 3KJQ B94 12.1951
12 3L9R L9Q 14.2857
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