Receptor
PDB id Resolution Class Description Source Keywords
1YKD 1.9 Å EC: 4.6.1.1 CRYSTAL STRUCTURE OF THE TANDEM GAF DOMAINS FROM A CYANOBACT ADENYLYL CYCLASE: NOVEL MODES OF LIGAND-BINDING AND DIMERIZ ANABAENA SP. GAF DOMAIN BOUND CYCLIC AMP LIGAND LYASE
Ref.: CRYSTAL STRUCTURE OF THE TANDEM GAF DOMAINS FROM A CYANOBACTERIAL ADENYLYL CYCLASE: MODES OF LIGAND BI DIMERIZATION PROC.NATL.ACAD.SCI.USA V. 102 3082 2005
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
CMP A:501;
A:502;
B:503;
B:504;
Valid;
Valid;
Valid;
Valid;
none;
none;
none;
none;
submit data
329.206 C10 H12 N5 O6 P c1nc(...
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90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
1YKD 1.9 Å EC: 4.6.1.1 CRYSTAL STRUCTURE OF THE TANDEM GAF DOMAINS FROM A CYANOBACT ADENYLYL CYCLASE: NOVEL MODES OF LIGAND-BINDING AND DIMERIZ ANABAENA SP. GAF DOMAIN BOUND CYCLIC AMP LIGAND LYASE
Ref.: CRYSTAL STRUCTURE OF THE TANDEM GAF DOMAINS FROM A CYANOBACTERIAL ADENYLYL CYCLASE: MODES OF LIGAND BI DIMERIZATION PROC.NATL.ACAD.SCI.USA V. 102 3082 2005
Members (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 9 families.
1 1YKD - 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 9 families.
1 1YKD - 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 8 families.
1 1YKD - 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 : 1YKD; Ligand: CMP; Similar sites found: 167
This union binding pocket(no: 1) in the query (biounit: 1ykd.bio1) has 20 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 4WG0 CHD 0.01243 0.41263 None
2 2VWA PTY 0.02667 0.40289 None
3 4ZGM 32M 0.01532 0.41531 0.819672
4 4XBA GMP 0.01231 0.40162 1
5 4XMF HSM 0.007186 0.4302 1.08696
6 5BU2 AMP 0.01028 0.42156 1.25628
7 4LSJ LSJ 0.0049 0.41414 1.55039
8 1M2Z DEX 0.00323 0.40376 1.55642
9 1IXI 2HP 0.01157 0.41977 1.55763
10 4P6X HCY 0.004529 0.41383 1.56863
11 2Q8H TF4 0.02627 0.40589 1.75879
12 2OS2 OGA 0.02382 0.40197 1.83727
13 5ISY NAD 0.009123 0.40773 1.9305
14 1GQG DCD 0.002036 0.43293 2
15 2Q1H AS4 0.006295 0.40563 2
16 1AUA BOG 0.0218 0.40177 2.02703
17 5FIT AP2 0.01317 0.40024 2.04082
18 3LA3 2FT 0.01442 0.41287 2.05761
19 5EXA 5SO 0.007114 0.42162 2.17391
20 5W0N UPU 0.009557 0.41999 2.26131
21 3HYW DCQ 0.01882 0.4068 2.26131
22 5FR0 SIZ 0.01042 0.40502 2.26131
23 4J6C STR 0.01903 0.40049 2.26131
24 3NW7 LGV 0.03039 0.40233 2.28013
25 2Y7P SAL 0.01171 0.41551 2.29358
26 3G58 988 0.01339 0.40385 2.3622
27 4QHP 32Q 0.007064 0.40707 2.51256
28 5MOB A8S 0.006774 0.41809 2.58621
29 1R6D DAU 0.03455 0.40563 2.67062
30 4BVA T3 0.01986 0.40681 2.68657
31 4J4H NAI 0.03285 0.40149 2.7027
32 2G30 ALA ALA PHE 0.002748 0.41686 2.71318
33 4ZW3 4S9 0.01964 0.40298 2.76382
34 3GN8 DEX 0.002343 0.4094 2.81124
35 2HZQ STR 0.01705 0.40861 2.87356
36 5JKG 6LF 0.01321 0.41325 2.89389
37 1XL8 152 0.001661 0.46056 3.01508
38 1OFL NGK GCD 0.006813 0.42886 3.01508
39 1Q19 SSC 0.02013 0.40199 3.01508
40 4Q0L V14 0.01031 0.40603 3.04183
41 2YMZ LAT 0.0009725 0.44323 3.07692
42 1XXR MAN 0.01712 0.40672 3.10559
43 4DE9 VTP 0.01163 0.409 3.14685
44 1WS1 BB2 0.003178 0.42059 3.20513
45 3D91 REM 0.02054 0.44751 3.22581
46 3ZGJ RMN 0.0151 0.4099 3.2345
47 5D9G GLU ASN LEU TYR PHE GLN 0.01712 0.40277 3.25203
48 5CX6 CDP 0.01017 0.42257 3.26633
49 5I49 2KH 0.009656 0.41069 3.26633
50 2RCU BUJ 0.0388 0.40311 3.26633
51 1EM6 NBG 0.03173 0.40058 3.26633
52 2XMY CDK 0.04156 0.40671 3.3557
53 4TS1 TYR 0.0184 0.40553 3.44828
54 3VQ2 LP4 LP5 MYR DAO 0.02885 0.40173 3.47222
55 2ET1 GLV 0.0002046 0.50694 3.48259
56 3DTU DXC 0.0127 0.41463 3.51759
57 4MRP GSH 0.03007 0.40478 3.51759
58 4RKK GLC GLC GLC GLC GLC GLC 0.00443 0.41817 3.61446
59 4I90 CHT 0.009633 0.42481 3.63036
60 2XVD AS6 0.005482 0.42141 3.64238
61 3FW3 ETS 0.01168 0.40671 3.7594
62 4DV8 0LX 0.006489 0.42563 3.76884
63 3ZJX BOG 0.007683 0.43031 3.80623
64 4N9I PCG 0.02572 0.40587 3.80952
65 3PUA OGA 0.01409 0.41348 3.82653
66 4R78 AMP 0.01417 0.40685 3.8835
67 2VFK AMP 0.00432 0.4365 3.90244
68 1OF4 BMA BMA BMA BMA BMA 0.02122 0.40398 3.91061
69 2WA4 069 0.01141 0.40316 4.01146
70 1N20 3AG 0.007576 0.40741 4.0201
71 5KOD IAC 0.01342 0.40301 4.0201
72 4MN7 SME 0.0006148 0.46807 4.02685
73 1ZZ7 S0H 0.00667 0.4279 4.0404
74 4J7Q B7N 0.01078 0.41526 4.2042
75 1SR7 MOF 0.001926 0.44648 4.2471
76 4NOS H4B 0.01266 0.4163 4.27136
77 3KO0 TFP 0.01398 0.41535 4.27136
78 2XN5 FUN 0.01571 0.4005 4.28571
79 4AZC NGW 0.02559 0.40083 4.29864
80 4MGD 27N 0.004064 0.41989 4.31373
81 2BJ4 OHT 0.003854 0.41693 4.36508
82 4TV1 36M 0.001032 0.46887 4.38247
83 1M13 HYF 0.005699 0.42463 4.43038
84 1I06 TZL 0.01132 0.41626 4.44444
85 5H9Q TD2 0.001416 0.44841 4.51613
86 4DR9 BB2 0.004522 0.41375 4.6875
87 4JHG ZEA 0.004652 0.4132 4.7619
88 4WOE ADP 0.005124 0.43618 4.77387
89 4ASE AV9 0.01141 0.40543 4.81586
90 1GVE CIT 0.00726 0.42721 4.89297
91 1QKQ MAN 0.01403 0.40064 4.92958
92 5HCN DAO 0.0184 0.40553 4.98084
93 3OBT SLB 0.00684 0.42062 5.02513
94 1JGS SAL 0.0166 0.43622 5.07246
95 1A78 TDG 0.0056 0.42539 5.22388
96 3TDC 0EU 0.005493 0.44041 5.27638
97 2E2R 2OH 0.003622 0.43751 5.27638
98 4BXF AKG 0.008095 0.4243 5.27638
99 2I74 MAN MAN MAN MAN 0.005487 0.43412 5.29101
100 4DSU BZI 0.007043 0.43013 5.29101
101 5G1N PAL 0.004593 0.41746 5.41401
102 3DFR MTX 0.009587 0.40672 5.55556
103 2QQC AG2 0.01268 0.41375 5.66038
104 4OCT AKG 0.01466 0.40195 5.77889
105 5CHR 4NC 0.01518 0.41113 5.83942
106 3B9Z CO2 0.03621 0.40126 6.03015
107 4X5S AZM 0.005765 0.43646 6.03448
108 1Q3A NGH 0.01125 0.41179 6.06061
109 5MWE TCE 0.0001567 0.5102 6.17284
110 5V4R MGT 0.005989 0.43497 6.17284
111 2I0G I0G 0.005773 0.44167 6.22568
112 2Q0D ATP 0.0122 0.40805 6.28141
113 3RLF MAL 0.008114 0.41881 6.41892
114 3A16 PXO 0.01514 0.40906 6.43432
115 2HHP FLC 0.004373 0.42976 6.53266
116 1XMY ROL 0.01916 0.40035 6.53266
117 2YJD YJD 0.002741 0.42346 6.66667
118 4COQ SAN 0.004807 0.43903 6.88259
119 1KGI T4A 0.007792 0.40849 7.08661
120 5AIG VPR 0.01058 0.40877 7.2
121 5N8V KZZ 0.006965 0.42208 7.24638
122 3WMX THR 0.005666 0.41334 7.26257
123 3P9T TCL 0.004946 0.42465 7.30594
124 1ULE GLA GAL NAG 0.01367 0.41039 7.33333
125 3M3E GAL A2G NPO 0.01222 0.4024 7.45342
126 4QYN RTL 0.009962 0.40209 7.5188
127 3TL1 JRO 0.001897 0.45552 7.54717
128 3WV6 GAL BGC 0.003594 0.42636 7.77027
129 3WV6 GAL GLC 0.001357 0.42022 7.77027
130 2OVD DAO 0.007925 0.42736 8.24176
131 1J78 VDY 0.01186 0.41066 8.29146
132 3K3K A8S 0.00273 0.40722 8.53081
133 5E58 CPZ 0.02321 0.40017 8.54271
134 3R9V DXC 0.01637 0.41052 8.74126
135 3AB4 THR 0.01348 0.40791 8.98876
136 2UXI G50 0.002288 0.41548 9.04762
137 1ECM TSA 0.0117 0.41095 9.17431
138 1C1L GAL BGC 0.003305 0.44377 9.48905
139 4L4J NAG NAG BMA MAN NAG 0.003513 0.43683 9.50226
140 3JRS A8S 0.001894 0.42094 9.61539
141 5UGW GSH 0.001635 0.41434 9.71429
142 1Y9Q MED 0.003693 0.44276 9.89583
143 3KDJ A8S 0.004647 0.40326 9.90099
144 4YEE 4CQ 0.01329 0.41471 10
145 5N17 8FK 0.01941 0.41361 10.1449
146 3E8T UQ8 0.004398 0.45067 11.3636
147 5L8N 6RQ 0.01546 0.41027 11.7188
148 1SW1 PBE 0.006662 0.4307 12.7273
149 2YKL NLD 0.007972 0.41048 13.6792
150 1WW5 SGA BGC 0.004064 0.44208 13.75
151 4MA6 28E 0.00509 0.43385 14.0127
152 3MB3 MB3 0.003783 0.40763 14.8148
153 2Y2B AH0 0.01252 0.41588 15.508
154 5DG2 GAL GLC 0.003272 0.4219 15.5556
155 1KJ1 MAN 0.01087 0.4161 15.5963
156 5N18 8HZ 0.02365 0.40176 15.5963
157 3MTX PGT 0.0148 0.40536 15.894
158 4R38 RBF 0.002543 0.40877 17.1429
159 3MMH SME 0.0002679 0.44023 17.3653
160 2IDO TMP 0.01579 0.41135 19.2771
161 1DZK PRZ 0.004239 0.415 19.7452
162 3NMV PYV 0.002963 0.41336 20.7865
163 3N7S 3N7 0.004644 0.44537 23.9583
164 5W10 CMP 0.00000001088 0.63843 37.9487
165 3SAO DBH 0.0129 0.41369 38.125
166 3SAO NKN 0.007014 0.40905 38.125
167 2ZMF CMP 0.000000002703 0.66421 48.1481
Pocket No.: 2; Query (leader) PDB : 1YKD; 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: 1ykd.bio1) has 20 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
Pocket No.: 3; Query (leader) PDB : 1YKD; 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: 1ykd.bio1) has 18 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
Pocket No.: 4; Query (leader) PDB : 1YKD; 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: 1ykd.bio1) has 17 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
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