Receptor
PDB id Resolution Class Description Source Keywords
4CYD 1.82 Å NON-ENZYME: OTHER GLXR BOUND TO CAMP SYNTHETIC CONSTRUCT TRANSCRIPTION TRANSCRIPTIONAL REGULATOR
Ref.: THE CRYSTAL STRUCTURES OF APO AND CAMP-BOUND GLXR F CORYNEBACTERIUM GLUTAMICUM REVEAL STRUCTURAL AND DY CHANGES UPON CAMP BINDING IN CRP/FNR FAMILY TRANSCR FACTORS. PLOS ONE V. 9 3265 2014
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
GOL A:1229;
A:1230;
Invalid;
Invalid;
none;
none;
submit data
92.094 C3 H8 O3 C(C(C...
CMP B:1228;
C:1228;
A:1228;
D:1226;
Valid;
Valid;
Valid;
Valid;
none;
none;
none;
none;
Kd = 17 uM
329.206 C10 H12 N5 O6 P c1nc(...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
4CYD 1.82 Å NON-ENZYME: OTHER GLXR BOUND TO CAMP SYNTHETIC CONSTRUCT TRANSCRIPTION TRANSCRIPTIONAL REGULATOR
Ref.: THE CRYSTAL STRUCTURES OF APO AND CAMP-BOUND GLXR F CORYNEBACTERIUM GLUTAMICUM REVEAL STRUCTURAL AND DY CHANGES UPON CAMP BINDING IN CRP/FNR FAMILY TRANSCR FACTORS. PLOS ONE V. 9 3265 2014
Members (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1256 families.
1 4CYD Kd = 17 uM CMP C10 H12 N5 O6 P c1nc(c2c(n....
70% Homology Family (2)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1068 families.
1 4CYD Kd = 17 uM CMP C10 H12 N5 O6 P c1nc(c2c(n....
2 3I59 - N6R C19 H22 N5 O6 P C[C@H](Cc1....
50% Homology Family (2)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 922 families.
1 4CYD Kd = 17 uM CMP C10 H12 N5 O6 P c1nc(c2c(n....
2 3I59 - N6R C19 H22 N5 O6 P C[C@H](Cc1....
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 : 4CYD; Ligand: CMP; Similar sites found: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 1) in the query (biounit: 4cyd.bio2) has 18 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
Pocket No.: 2; Query (leader) PDB : 4CYD; Ligand: CMP; Similar sites found: 33
This union binding pocket(no: 2) in the query (biounit: 4cyd.bio2) has 19 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 3B6R CRN 0.01321 0.41803 2.66667
2 2RH1 CAU 0.008098 0.40244 3.11111
3 2RKV ZBA 0.02831 0.40051 3.55556
4 2AE2 PTO 0.0285 0.40412 4.88889
5 2AE2 NAP 0.0285 0.40412 4.88889
6 5ECP MET 0.01627 0.41422 14.2857
7 5ECP JAA 0.01627 0.41422 14.2857
8 5ECP ATP 0.01702 0.41422 14.2857
9 3RDE OYP 0.01169 0.40238 14.6667
10 1CX4 CMP 0.00000004893 0.63511 17.7778
11 3JUC PCA 0.01407 0.41062 19.0476
12 3OF1 CMP 0.000001312 0.53638 19.5556
13 5H5O PCG 0.00001446 0.51368 20.9302
14 1NE6 SP1 0.0000001451 0.61063 21.7778
15 3SHR CMP 0.0000002419 0.62778 22.2222
16 4NVP 7CH 0.0000001434 0.59871 24.4444
17 4AVB CMP 0.0000008077 0.55641 25.7778
18 5BV6 35G 0.0000004413 0.59568 28.9474
19 5K8S CMP 0.00000006992 0.6282 29.0541
20 3PNA CMP 0.0000007768 0.53248 29.2208
21 5KBF CMP 0.00000005648 0.61654 30.2222
22 4KU7 PCG 0.0000002379 0.6186 31.3725
23 3OCP CMP 0.00000007412 0.5886 33.0935
24 5KJZ PCG 0.00000009444 0.61889 33.3333
25 4OFG PCG 0.00000003995 0.61082 34.0278
26 5JAX 6J7 0.0000002297 0.60179 35.5556
27 5C8W PCG 0.000000415 0.55018 41.958
28 2XHK AKG 0.0002185 0.4438 44.5946
29 2XKO AKG 0.0004193 0.42263 44.5946
30 3LA3 2FT 0.000419 0.42094 45.7778
31 3KCC CMP 0.00000001737 0.65868 46.2222
32 2GAG FOA 0.03596 0.40326 47.619
33 2GAG FAD 0.03875 0.40163 47.619
34 4N9I PCG 0.000009809 0.57708 50
Pocket No.: 3; Query (leader) PDB : 4CYD; Ligand: CMP; Similar sites found: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 3) in the query (biounit: 4cyd.bio1) has 18 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
Pocket No.: 4; Query (leader) PDB : 4CYD; Ligand: CMP; Similar sites found: 6
This union binding pocket(no: 4) in the query (biounit: 4cyd.bio1) has 19 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 5A5W GUO 0.03273 0.40025 1.97628
2 3UOY NAP 0.04291 0.41168 3.11111
3 3UOY FAD 0.04291 0.41168 3.11111
4 5HX8 66P 0.01558 0.40113 4.44444
5 5UR1 YY9 0.02277 0.40893 16.4444
6 2H6B 3C4 0.009681 0.41075 33.7778
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