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 250 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 217 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 181 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: 94
No: Ligand ECFP6 Tc MDL keys Tc
1 CMP 1 1
2 2BA 1 0.984848
3 SP1 0.757143 0.928571
4 RP1 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 N6S 0.535354 0.914286
14 N6R 0.535354 0.914286
15 C2E 0.534091 0.902778
16 35G 0.534091 0.888889
17 PCG 0.534091 0.888889
18 1YC 0.53 0.875
19 Y3J 0.506667 0.753623
20 5CD 0.5 0.811594
21 XYA 0.5 0.826087
22 ACK 0.5 0.897059
23 ADN 0.5 0.826087
24 RAB 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 AMP 0.447059 0.927536
37 A 0.447059 0.927536
38 QQY 0.447059 0.847222
39 3DH 0.440476 0.777778
40 AMP MG 0.436782 0.875
41 3AM 0.435294 0.913043
42 ABM 0.431818 0.901408
43 J7C 0.431818 0.75
44 A2D 0.431818 0.928571
45 ZAS 0.430233 0.77027
46 7D7 0.428571 0.771429
47 S4M 0.426966 0.666667
48 6RE 0.425287 0.74026
49 SRA 0.425287 0.876712
50 3AD 0.425 0.838235
51 2AM 0.423529 0.9
52 AP2 0.422222 0.864865
53 A12 0.422222 0.864865
54 BA3 0.422222 0.928571
55 MAO 0.422222 0.740741
56 NEC 0.420455 0.726027
57 A3G 0.420455 0.780822
58 DSH 0.420455 0.727273
59 AOC 0.420455 0.802817
60 BEF ADP 0.419355 0.84
61 SFG 0.419355 0.753425
62 ADP BEF 0.419355 0.84
63 6JR 0.419048 0.927536
64 B4P 0.417582 0.928571
65 5AS 0.417582 0.741176
66 AP5 0.417582 0.928571
67 ADP 0.417582 0.901408
68 A3N 0.41573 0.767123
69 APC 0.414894 0.864865
70 SON 0.413043 0.864865
71 AN2 0.413043 0.888889
72 EEM 0.412371 0.691358
73 GJV 0.411111 0.730769
74 GGZ 0.41 0.78481
75 OVE 0.409091 0.863014
76 ADP MG 0.408602 0.863014
77 AU1 0.408602 0.876712
78 M33 0.408602 0.888889
79 CA0 0.408602 0.876712
80 ADX 0.408602 0.810127
81 A3P 0.406593 0.927536
82 5X8 0.404255 0.767123
83 50T 0.404255 0.888889
84 ATP 0.404255 0.901408
85 ACP 0.404255 0.876712
86 VO4 ADP 0.40404 0.888889
87 ADP VO4 0.40404 0.888889
88 SAM 0.402062 0.691358
89 0UM 0.401961 0.7
90 AQP 0.4 0.901408
91 APR 0.4 0.901408
92 PRX 0.4 0.876712
93 AR6 0.4 0.901408
94 5FA 0.4 0.901408
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 5W10; Ligand: CMP; Similar sites found: 91
This union binding pocket(no: 1) in the query (biounit: 5w10.bio1) has 21 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 4K55 H6P 0.000135 0.51551 None
2 3BU1 HSM 0.01257 0.4069 None
3 1N5S ADL 0.009292 0.40168 None
4 3QXV MTX 0.005399 0.40032 None
5 5ISY NAD 0.006944 0.41525 1.53846
6 2OVD DAO 0.02362 0.40442 1.64835
7 2D6M LBT 0.002761 0.44594 1.88679
8 5F6U 5VK 0.002464 0.44816 1.91083
9 4GQP B40 0.01423 0.41002 2.00803
10 3BRN SRO 0.02108 0.40622 2.54777
11 3BF8 MLA 0.001784 0.45681 2.5641
12 1OFL NGK GCD 0.001933 0.44992 2.5641
13 4RDL FUC GAL NDG FUC 0.01863 0.40988 2.5641
14 5J75 6GQ 0.003307 0.404 2.5641
15 2NSX IFM 0.005004 0.42195 3.07692
16 4FBL SPD 0.009835 0.41659 3.07692
17 1DMY AZM 0.01341 0.40989 3.07692
18 3BOF HCS 0.01934 0.4078 3.07692
19 4H6B 10X 0.01345 0.40169 3.07692
20 1Q8A HCS 0.02487 0.40168 3.07692
21 5LUN OGA 0.003407 0.43447 3.58974
22 5T8U LPA 0.01043 0.4069 3.58974
23 3G0I VPR 0.01953 0.40604 3.58974
24 3T4L ZEA 0.00655 0.40487 3.58974
25 2IXC TRH 0.007868 0.40159 3.58974
26 1J3R 6PG 0.007755 0.41721 3.68421
27 2GC0 PAN 0.006541 0.4049 3.7234
28 1MDC PLM 0.006584 0.40667 3.78788
29 3QRC SCR 0.01261 0.41029 3.82166
30 5JJ2 MLI 0.005085 0.45853 4.10256
31 3ML5 AZM 0.01075 0.42282 4.10256
32 5A5W GUO 0.008712 0.42154 4.10256
33 1QKQ MAN 0.0006869 0.41716 4.22535
34 4RT1 C2E 0.009829 0.40058 4.46429
35 2YMZ LAT 0.001215 0.47498 4.61538
36 1Z03 OCH 0.005036 0.43608 4.61538
37 3ZJX BOG 0.006703 0.43539 4.61538
38 4KBA 1QM 0.01893 0.40244 4.61538
39 5W4W 9WG 0.001803 0.40238 4.61538
40 1ZGS XMM 0.03085 0.40076 4.61538
41 4WVW SLT 0.000609 0.48443 4.86111
42 1DZK PRZ 0.005093 0.41344 5.09554
43 5D9G GLU ASN LEU TYR PHE GLN 0.004938 0.43143 5.12821
44 1S7G APR 0.008033 0.41673 5.12821
45 4DSU BZI 0.00324 0.44868 5.29101
46 1P0Z FLC 0.002495 0.45345 5.34351
47 5G1N PAL 0.009524 0.40488 5.64103
48 3KO0 TFP 0.02561 0.40244 5.94059
49 5KOD IAC 0.001723 0.44829 6.15385
50 3VP6 HLD 0.006234 0.41094 6.15385
51 5JSP DQY 0.01656 0.40994 6.15385
52 5FBN 5WF 0.01269 0.40762 6.15385
53 3VV1 GAL FUC 0.006009 0.43666 6.25
54 4K7O EKZ 0.02403 0.40253 6.54762
55 4F4P 0SB 0.03845 0.40257 6.66667
56 5H2U 1N1 0.008463 0.40351 6.74157
57 4X5S AZM 0.009266 0.42821 7.17949
58 4L6H HCS 0.02455 0.40309 7.17949
59 5KJW 53C 0.003056 0.44216 8.20513
60 5LXB 7A9 0.00935 0.42407 8.20513
61 3OYW TDG 0.004386 0.43913 8.20895
62 4HIA FMN 0.01761 0.40215 8.52273
63 1LSH PLD 0.005362 0.41968 8.71795
64 1DRJ RIP 0.01906 0.40783 8.71795
65 1ZM1 BGC BGC BGC 0.006421 0.40891 9.23077
66 3A16 PXO 0.0007283 0.48369 9.74359
67 5L2J 6UL 0.01765 0.42309 9.74359
68 5L2J 70E 0.01867 0.42309 9.74359
69 2QRY TPS 0.008321 0.40029 9.74359
70 2YKL NLD 0.002836 0.43357 9.90566
71 2G30 ALA ALA PHE 0.00007186 0.49667 10.2564
72 5DCH 1YO 0.0237 0.40331 10.2564
73 2XKO AKG 0.006677 0.43287 10.3604
74 3LA3 2FT 0.006486 0.43367 10.7692
75 2YKX AKG 0.02162 0.40148 10.7692
76 5TVM PUT 0.005842 0.43321 11.2821
77 3MBI HSX 0.01872 0.40268 11.7949
78 4Y24 TD2 0.01252 0.40714 12.3377
79 3IWD M2T 0.008433 0.42468 13.2353
80 4LRJ ANP 0.006237 0.40948 14.2012
81 2DUR MAN MAN 0.01045 0.42291 14.359
82 3ANY 2A3 0.02148 0.40431 14.359
83 1YFS ALA 0.0007516 0.48513 16.4103
84 4WOE ADP 0.006374 0.43331 16.4103
85 5H9Q TD2 0.006646 0.42637 16.7742
86 3MMH SME 0.0001556 0.49907 17.9641
87 3A76 SPD 0.01373 0.41577 20.4545
88 1A78 TDG 0.007447 0.42692 27.6119
89 4MN7 SME 0.003072 0.43663 29.5302
90 1YKD CMP 0.00000001088 0.63843 37.9487
91 2ZMF CMP 0.000000000002788 0.8036 39.1534
Pocket No.: 2; Query (leader) PDB : 5W10; Ligand: CMP; Similar sites found: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 2) in the query (biounit: 5w10.bio1) has 21 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
Pocket No.: 3; Query (leader) PDB : 5W10; Ligand: CMP; Similar sites found: 16
This union binding pocket(no: 3) in the query (biounit: 5w10.bio2) has 21 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 4USI AKG 0.02043 0.40203 None
2 1GQG DCD 0.006808 0.40604 2.05128
3 1Y7P RIP 0.001228 0.46568 3.07692
4 3WV6 GAL BGC 0.002561 0.45411 3.07692
5 3HQP OXL 0.0324 0.406 3.07692
6 5HES 032 0.008984 0.40075 3.58974
7 3QP8 HL0 0.004749 0.41101 3.80435
8 4XMF HSM 0.0005841 0.49248 4.34783
9 4XV1 904 0.01649 0.40124 5.47945
10 4L3L 5FI 0.01392 0.40097 6.15385
11 5KEW 6SB 0.01962 0.40786 6.25
12 4S1D 41M 0.004643 0.43787 6.66667
13 5U98 1KX 0.01449 0.41119 8.08081
14 5OFW 9TW 0.02459 0.40224 9.23077
15 5DG2 GAL GLC 0.002056 0.4516 9.62963
16 4OKD GLC GLC GLC 0.02472 0.40111 9.74359
Pocket No.: 4; Query (leader) PDB : 5W10; Ligand: CMP; Similar sites found: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 4) in the query (biounit: 5w10.bio2) has 21 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
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