Receptor
PDB id Resolution Class Description Source Keywords
5KBF 2 Å EC: 2.7.11.11 CAMP BOUND PFPKA-R (141-441) PLASMODIUM FALCIPARUM (ISOLATE 3D7) PLASMODIUM FALCIPARUM PKA PROTEIN KINASE A CAMP CBD CYCNUCLEOTIDE BINDING CNB REGULATORY DOMAIN R TRANSFERASE
Ref.: DISRUPTING THE ALLOSTERIC INTERACTION BETWEEN THE P FALCIPARUM CAMP-DEPENDENT KINASE AND ITS REGULATORY J. BIOL. CHEM. V. 291 25375 2016
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
CMP B:501;
B:502;
A:501;
A:502;
Valid;
Valid;
Valid;
Valid;
none;
none;
none;
none;
Kd = 1.2 nM
329.206 C10 H12 N5 O6 P c1nc(...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
5KBF 2 Å EC: 2.7.11.11 CAMP BOUND PFPKA-R (141-441) PLASMODIUM FALCIPARUM (ISOLATE 3D7) PLASMODIUM FALCIPARUM PKA PROTEIN KINASE A CAMP CBD CYCNUCLEOTIDE BINDING CNB REGULATORY DOMAIN R TRANSFERASE
Ref.: DISRUPTING THE ALLOSTERIC INTERACTION BETWEEN THE P FALCIPARUM CAMP-DEPENDENT KINASE AND ITS REGULATORY J. BIOL. CHEM. V. 291 25375 2016
Members (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 9 families.
1 5KBF Kd = 1.2 nM 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 8 families.
1 5KBF Kd = 1.2 nM CMP C10 H12 N5 O6 P c1nc(c2c(n....
50% Homology Family (9)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 12 families.
1 5J48 - 6FW C16 H15 Cl N5 O7 P S c1cc(ccc1S....
2 3PNA - CMP C10 H12 N5 O6 P c1nc(c2c(n....
3 5KJY - CMP C10 H12 N5 O6 P c1nc(c2c(n....
4 5T3N Kd = 9.1 nM 75G C10 H11 Cl N5 O5 P S c1nc2c(nc(....
5 5JIX - 6J7 C10 H11 Br N5 O7 P C1[C@@H]2[....
6 1NE6 - SP1 C10 H12 N5 O5 P S c1nc(c2c(n....
7 1NE4 - RP1 C10 H12 N5 O5 P S c1nc(c2c(n....
8 5KBF Kd = 1.2 nM CMP C10 H12 N5 O6 P c1nc(c2c(n....
9 1CX4 - 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 : 5KBF; Ligand: CMP; Similar sites found: 55
This union binding pocket(no: 1) in the query (biounit: 5kbf.bio1) has 18 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 3B8Y ADA ADA ADA ADA 0.00617 0.42041 1.66113
2 4JGT PYR 0.01283 0.41999 1.67224
3 4XOE KGM 0.01388 0.40852 1.79211
4 4KYS VIB 0.01176 0.41134 1.99336
5 5EXK 5AD 0.02163 0.401 2.32558
6 1O5Q PYR 0.008086 0.41948 2.65781
7 1WD4 AHR 0.01493 0.40169 2.99003
8 5HES 032 0.004629 0.4248 3.32226
9 3HAV ATP 0.01111 0.41397 3.34448
10 2J5V PCA 0.02163 0.40039 3.65448
11 4X1B MLI 0.01513 0.41917 3.98671
12 1VPD TLA 0.01147 0.41026 4.01338
13 1H6H PIB 0.01122 0.4123 4.1958
14 3WG3 A2G GAL NAG FUC 0.007608 0.42372 4.49438
15 1T9D P22 0.0127 0.40965 4.65116
16 1RYO OXL 0.01329 0.40456 5.31561
17 2W3L DRO 0.02123 0.40086 5.55556
18 1D8C GLV 0.02106 0.40279 5.64784
19 2ZV2 609 0.004812 0.4209 5.7047
20 5T7I LAT NAG GAL 0.02049 0.40089 5.80645
21 5AB1 BCD TA5 HP6 MAN 0.01317 0.40644 6
22 4OKD GLC GLC GLC 0.01843 0.40125 6.31229
23 5XNA SHV 0.01877 0.40743 6.52174
24 3JUC PCA 0.0192 0.40141 6.53595
25 1KSK URA 0.01753 0.41029 6.83761
26 4Z7X 3CX 0.002258 0.45622 7.14286
27 4Y8D 49J 0.004542 0.40121 7.14286
28 4YMJ 4EJ 0.01065 0.41572 7.30897
29 1Q19 SSC 0.008131 0.42488 7.6412
30 4NFN 2KC 0.001836 0.42279 8.30565
31 1LCF OXL 0.01676 0.40657 8.30565
32 3MTX PGT 0.008142 0.42943 8.60927
33 5UIU 8CG 0.01097 0.41595 10.299
34 4K7O EKZ 0.03234 0.40005 12.5
35 5H2U 1N1 0.006183 0.40038 14.6067
36 4AVB CMP 0.000000003908 0.69732 15.2824
37 2OX9 GAL NAG FUC 0.009167 0.40642 16.4286
38 5CAD PCA 0.007071 0.4268 16.6113
39 3LA3 2FT 0.001948 0.45208 19.7531
40 2XKO AKG 0.001095 0.46445 22.0721
41 2XHK AKG 0.003065 0.44055 22.0721
42 3CF6 SP1 0.0000005079 0.57689 22.9236
43 3KCC CMP 0.00000001078 0.61387 24.2308
44 3I54 CMP 0.00000009734 0.6064 24.498
45 3I59 N6S 0.0000003768 0.55354 24.498
46 3I59 N6R 0.0000004557 0.54891 24.498
47 4CYD CMP 0.00000005648 0.61654 30.2222
48 5H5O PCG 0.0001014 0.48771 31.7829
49 5KEW 6SB 0.01063 0.41609 31.9149
50 4MUV PCG 0.00000000151 0.68371 38.0282
51 4OFG PCG 0.0000000001215 0.76684 41.6667
52 4KU7 PCG 0.0000000005625 0.73615 43.7908
53 3SHR CMP 0.000000001164 0.73382 45.485
54 5JAX 6J7 0.000000001331 0.68631 46.6667
55 3OCP CMP 0.0000000004489 0.75338 48.2014
Pocket No.: 2; Query (leader) PDB : 5KBF; 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: 5kbf.bio1) has 15 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
Pocket No.: 3; Query (leader) PDB : 5KBF; 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: 5kbf.bio2) has 15 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
Pocket No.: 4; Query (leader) PDB : 5KBF; Ligand: CMP; Similar sites found: 10
This union binding pocket(no: 4) in the query (biounit: 5kbf.bio2) has 18 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 1IT7 GUN 0.004962 0.42027 2.32558
2 5CDH TLA 0.01195 0.40633 2.65781
3 4WOE 3S5 0.01756 0.40098 3.98671
4 3WMX THR 0.02652 0.41231 4.98339
5 4D42 NAP 0.04968 0.40203 5.64784
6 4D42 W0I 0.04968 0.40203 5.64784
7 1NVM OXL 0.01711 0.40234 6.41026
8 3OV6 MK0 0.02008 0.40449 6.64452
9 5O4J SAH 0.02026 0.40884 6.93431
10 5O4J 9KH 0.02026 0.40884 6.93431
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