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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 (4)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 10 families.
1 3PNA - CMP C10 H12 N5 O6 P c1nc(c2c(n....
2 1NE6 - SP1 C10 H12 N5 O5 P S c1nc(c2c(n....
3 1NE4 - RP1 C10 H12 N5 O5 P S c1nc(c2c(n....
4 5KBF Kd = 1.2 nM 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 : 5KBF; Ligand: CMP; Similar sites found with APoc: 141
This union binding pocket(no: 1) in the query (biounit: 5kbf.bio1) has 18 residues
No: Leader PDB Ligand Sequence Similarity
1 2CHT TSA 1.5748
2 1RRC ADP 1.66113
3 3B8Y ADA ADA ADA ADA 1.66113
4 4JGT PYR 1.67224
5 4XOE KGM 1.79211
6 4KYS VIB 1.99336
7 4LIK CIT 2.32558
8 4AG8 AXI 2.32558
9 4ASE AV9 2.32558
10 5EXK 5AD 2.32558
11 5UL5 8D7 2.32558
12 5UL5 PLM 2.32558
13 3RG9 WRA 2.5
14 3RG9 NDP 2.5
15 3NOJ PYR 2.52101
16 2AEL SAZ 2.65781
17 1O5Q PYR 2.65781
18 6E2O S0L 2.71186
19 3VRV YSD 2.95203
20 4D4U FUC 2.99003
21 4R5Z PMP 2.99003
22 1WD4 AHR 2.99003
23 3EEL 53T 3.0837
24 5VC5 96M 3.11419
25 2CIG 1DG 3.14465
26 5UC1 486 3.15315
27 1LBF 137 3.23887
28 4QMN DB8 3.32226
29 3KJS DQ1 3.32226
30 3HAV ATP 3.34448
31 2VWT PYR 3.37079
32 3THR C2F 3.41297
33 3TTC ADP 3.50076
34 4B5W PYR 3.51562
35 2J5V PCA 3.65448
36 3WG6 NDP 3.65448
37 4H8N NDP 3.65448
38 4XV1 904 3.76712
39 2FZH DH1 3.8835
40 1WUU GLA 3.98671
41 4X1B MLI 3.98671
42 3VRY B43 3.98671
43 3GE7 AFQ 3.98671
44 4DP3 MMV 3.98671
45 4DP3 NDP 3.98671
46 5FBN 5WF 4.05904
47 1H6H PIB 4.1958
48 5DEX GLY 4.24028
49 4EUE NAI 4.31894
50 2HK5 1BM 4.44444
51 3WG3 A2G GAL NAG FUC 4.49438
52 4R57 ACO 4.54545
53 1T9D P22 4.65116
54 2WLG SOP 4.65116
55 3OVR 5SP 4.82456
56 5QIN J2V 4.98339
57 5E58 CPZ 4.98339
58 5NDF UDP 4.98339
59 2CYC TYR 5.31561
60 4EUU BX7 5.31561
61 1RYO OXL 5.31561
62 2W3L DRO 5.55556
63 3AB4 THR 5.61798
64 2GTE VA 5.64516
65 1VJY 460 5.64784
66 1D8C GLV 5.64784
67 1SDW IYT 5.64784
68 2ZV2 609 5.7047
69 3A4M ADP 5.76923
70 5T7I LAT NAG GAL 5.80645
71 6BGC BGC 5.98007
72 2X2M X2M 5.98007
73 3B6C SDN 5.98291
74 5AB1 BCD TA5 HP6 MAN 6
75 3AD8 FAD 6.06061
76 3AD8 PYC 6.06061
77 5AEW BNL 6.31229
78 3V8S 0HD 6.31229
79 5JFL NAD 6.31229
80 4AT0 FAD 6.31229
81 4OKD GLC GLC GLC 6.31229
82 2FLI DX5 6.36364
83 1NVM OXL 6.41026
84 5XNA SHV 6.52174
85 3JUC PCA 6.53595
86 5TIV A3P 6.71937
87 5EYK 5U5 6.77966
88 3A76 SPD 6.81818
89 1KSK URA 6.83761
90 6GQM F8H 6.97674
91 3TTI KBI 6.97674
92 4Z7X 3CX 7.14286
93 4Y8D 49J 7.14286
94 4YMJ 4EJ 7.30897
95 1Q19 SSC 7.6412
96 4U0I 0LI 7.6412
97 6F3G CJN 7.79661
98 2Y6O 1N1 7.90378
99 3EKK GS2 7.97342
100 4EWH T77 8
101 4F7E 0SH 8.16327
102 4NFN 2KC 8.30565
103 2XK9 XK9 8.30565
104 1LCF OXL 8.30565
105 3MTX PGT 8.60927
106 4C2V YJA 9.09091
107 1ZB6 GST 9.30233
108 1U1I NAD 9.30233
109 5UIU 8CG 10.299
110 3PP0 03Q 11.2957
111 6GIN IR2 11.2957
112 4K7O EKZ 12.5
113 4CRL C1I 12.9825
114 5H2U 1N1 14.6067
115 4AVB CMP 15.2824
116 4YZC STU 15.9468
117 2OX9 GAL NAG FUC 16.4286
118 5CAD PCA 16.6113
119 3SXS PP2 17.1642
120 3LA3 2FT 19.7531
121 2XKO AKG 22.0721
122 2XHK AKG 22.0721
123 3CF6 SP1 22.9236
124 3KCC CMP 24.2308
125 3I54 CMP 24.498
126 3I59 N6S 24.498
127 3I59 N6R 24.498
128 5FII PHE 25.4902
129 4NVP 7CH 25.8373
130 2PTM CMP 26.2626
131 4N9I PCG 27.619
132 4CYD CMP 30.2222
133 5H5O PCG 31.7829
134 5KEW 6SB 31.9149
135 3VPB ADP 32.1429
136 4MUV PCG 38.0282
137 4OFG PCG 41.6667
138 4KU7 PCG 43.7908
139 3SHR CMP 45.485
140 5JAX 6J7 46.6667
141 3OCP CMP 48.2014
Pocket No.: 2; Query (leader) PDB : 5KBF; Ligand: CMP; Similar sites found with APoc: 100
This union binding pocket(no: 2) in the query (biounit: 5kbf.bio1) has 15 residues
No: Leader PDB Ligand Sequence Similarity
1 3B8I OXL 1.39373
2 3UOY NAP 1.66113
3 3UOY FAD 1.66113
4 4AUA 4AU 1.66113
5 5T79 NDP 1.66113
6 3MAG 3MA 1.99336
7 4G2R H1L 1.99336
8 2VHJ ADP 1.99336
9 5LXM ADP 2.12014
10 3CTL S6P 2.1645
11 5EPO TUD 2.29008
12 1IT7 GUN 2.32558
13 2B9I ADP 2.32558
14 5K4W NAI 2.32558
15 2B9J ADP 2.32558
16 6G33 5ID 2.32558
17 2B9F ADP 2.32558
18 5CDH TLA 2.65781
19 6FX0 E9T 2.65781
20 1OFZ FUC 2.65781
21 4MZU COA 2.65781
22 5NUE NAD 2.99003
23 5NUF NAD 2.99003
24 4K33 ACP 2.99003
25 5JKG 6LF 3.32226
26 4LOO SB4 3.32226
27 5HES 032 3.32226
28 1PVN MZP 3.32226
29 3GC8 B45 3.32226
30 1VBH PEP 3.32226
31 3N3T C2E 3.40136
32 2XZ9 PYR 3.65448
33 5UAO FAD 3.98671
34 2H8H H8H 3.98671
35 1KJ8 GAR 3.98671
36 1KJ8 ATP 3.98671
37 2IHT TPP 3.98671
38 3H78 BE2 3.98671
39 5BSZ SAH 4
40 3G5D 1N1 4.1958
41 1FCZ 156 4.25532
42 16PK BIS 4.31894
43 2OFV 242 4.33213
44 2FHK MFN 4.39189
45 4P83 U5P 4.3956
46 3RFV 15L 4.49438
47 3CV6 HXS 4.65116
48 3CV6 NAP 4.65116
49 3LXN MI1 4.65116
50 4F4P 0SB 4.7619
51 4X17 SIA 4.77941
52 4X17 SIA SIA 4.77941
53 4X7Q 3YR 4.80769
54 1REO FAD 4.98339
55 2Q1W NAD 4.98339
56 3WMX THR 4.98339
57 5MJA 7O3 5.31561
58 4BHL ARG 5.31561
59 1NM5 NAD 5.41872
60 2VSS V55 5.43478
61 4ZY1 4U5 5.64784
62 5E70 RCD 5.64784
63 3ZOK NAD 5.64784
64 1GUZ NAD 5.64784
65 3G5S FAD 5.64784
66 5DEY 59T 5.72391
67 3CR3 ADP 5.78512
68 5G57 6M5 5.98007
69 2VN9 GVD 5.98007
70 4WQM FAD 5.98007
71 2GAG FOA 6.06061
72 2GAG FAD 6.06061
73 1QFT HSM 6.28571
74 4P5Z Q7M 6.64452
75 1O9U ADZ 6.64452
76 4PLT OXM 6.64452
77 3E7O 35F 6.97674
78 5TA6 79D 6.97674
79 1T8U UAP SGN IDS SGN 6.98529
80 5USZ SKE 7.26644
81 4WNK 453 7.30897
82 5ZCT ANP 7.30897
83 4WGF HX2 7.31707
84 5DH3 5BS 7.6412
85 1Q3Q ANP 7.6412
86 2HJR APR 7.92683
87 3V66 D3A 7.97342
88 6ES0 BW8 10.299
89 1TI7 NAP 10.299
90 2VUT NAD 10.299
91 4UXL 5P8 10.8696
92 5WO4 B7V 11.9601
93 3WXM GTP 11.9601
94 1OPK P16 12.9568
95 3KRL KRL 13.289
96 2O07 SPD 13.9535
97 2O07 MTA 13.9535
98 5YJI SAH 16.5493
99 3OH3 UAD 16.6113
100 2J9C ATP 31.0924
Pocket No.: 3; Query (leader) PDB : 5KBF; Ligand: CMP; Similar sites found with APoc: 37
This union binding pocket(no: 3) in the query (biounit: 5kbf.bio2) has 15 residues
No: Leader PDB Ligand Sequence Similarity
1 4TM3 FAD 1.99336
2 5WS9 AMP 1.99336
3 5K2M ADP 2.1978
4 2F57 23D 2.32558
5 5K4W THR 2.32558
6 1V0O INR 2.43056
7 4L9Z COA 2.65781
8 1ZEM NAD 2.67176
9 1Q0H NDP 2.99003
10 4DM8 REA 2.99625
11 1KPH 10A 3.48432
12 1KPG 16A 3.48432
13 6AMI TRP 3.65448
14 1H82 FAD 3.98671
15 1H82 GZZ 3.98671
16 4LHD GLY 3.98671
17 3FSY SCA 4.31894
18 3RFV NAI 4.49438
19 6CQF F97 4.7138
20 4S3R 7SA 4.98339
21 1HYH NAD 5.64784
22 5HVJ ANP 5.64784
23 4OIV XX9 5.75221
24 1JQ9 PHE LEU SER TYR LYS 5.78512
25 2VZ6 FEF 5.98007
26 2XVD AS6 6.64452
27 4PLT NAI 6.64452
28 5Y6Q MCN 6.79012
29 5VCV 1N1 7.30897
30 4GJ3 0XP 7.61589
31 2DC1 NAD 7.62712
32 5U6C 7YS 8.63787
33 5XVG 8FX 8.87372
34 3RE4 TO1 8.91473
35 2JDR GLY ARG PRO ARG THR THR SER PHE ALA GLU 9.30233
36 2JDR L20 9.30233
37 5YJI 8WO 16.5493
Pocket No.: 4; Query (leader) PDB : 5KBF; Ligand: CMP; Similar sites found with APoc: 24
This union binding pocket(no: 4) in the query (biounit: 5kbf.bio2) has 18 residues
No: Leader PDB Ligand Sequence Similarity
1 1JCM 137 1.9305
2 5JFS 6K0 1.99336
3 3VHE 42Q 2.32558
4 2ZZV LAC 2.65781
5 4POW OP1 3.01887
6 1C3X 8IG 3.38346
7 4WOE 3S5 3.98671
8 2RG0 CBI 4.31894
9 5BVE 4VG 4.98339
10 2J0W ASP 5.31561
11 4D42 NAP 5.64784
12 4D42 W0I 5.64784
13 3FPF MTA 5.7047
14 3FPF TNA 5.7047
15 3MVH WFE 5.98007
16 3OV6 MK0 6.64452
17 5O4J SAH 6.93431
18 5O4J 9KH 6.93431
19 4IXW IXW 7.08661
20 5NKB 8ZT 7.30897
21 3VZ3 SSN 7.6412
22 4TWP AXI 7.74908
23 4A4X JUP 8.96057
24 5V6F MAN BMA MAN 10.1449
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