Receptor
PDB id Resolution Class Description Source Keywords
4FT8 1.97 Å NON-ENZYME: TRANSCRIPT_TRANSLATE E. COLI CATABOLITE ACTIVATOR PROTEIN WITH COBALT AND SULFATE ESCHERICHIA COLI WINGED HELIX-TURN-HELIX DNA BINDING PROTEIN COBALT BINDINGBINDING TRANSCRIPTION ACTIVATOR
Ref.: STRUCTURE OF CATABOLITE ACTIVATOR PROTEIN WITH COBA AND SULFATE. ACTA CRYSTALLOGR F STRUCT V. 70 560 2014 BIOL COMMUN
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
SO4 A:305;
A:304;
A:303;
B:304;
A:302;
B:303;
B:307;
A:307;
B:308;
B:305;
B:302;
A:306;
B:306;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
submit data
96.063 O4 S [O-]S...
CO B:309;
A:308;
Part of Protein;
Part of Protein;
none;
none;
submit data
58.933 Co [Co+2...
CMP A:301;
B:301;
Valid;
Valid;
none;
none;
submit data
329.206 C10 H12 N5 O6 P c1nc(...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
4N9I 2.19 Å NON-ENZYME: TRANSCRIPT_TRANSLATE CRYSTAL STRUCTURE OF TRANSCRIPTION REGULATION PROTEIN CRP CO WITH CGMP ESCHERICHIA COLI DNA BINDING TRANSCRIPTION REGULATOR
Ref.: STRUCTURES OF INACTIVE CRP SPECIES REVEAL THE ATOMI OF THE ALLOSTERIC TRANSITION THAT DISCRIMINATES CYC NUCLEOTIDE SECOND MESSENGERS. ACTA CRYSTALLOGR.,SECT.D V. 70 1726 2014
Members (14)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 257 families.
1 4I09 - CMP C10 H12 N5 O6 P c1nc(c2c(n....
2 4HZF - CMP C10 H12 N5 O6 P c1nc(c2c(n....
3 2GZW - CMP C10 H12 N5 O6 P c1nc(c2c(n....
4 4I0B - CMP C10 H12 N5 O6 P c1nc(c2c(n....
5 1HW5 - CMP C10 H12 N5 O6 P c1nc(c2c(n....
6 4FT8 - CMP C10 H12 N5 O6 P c1nc(c2c(n....
7 1I5Z - CMP C10 H12 N5 O6 P c1nc(c2c(n....
8 1G6N - CMP C10 H12 N5 O6 P c1nc(c2c(n....
9 4I02 - CMP C10 H12 N5 O6 P c1nc(c2c(n....
10 1I6X - CMP C10 H12 N5 O6 P c1nc(c2c(n....
11 4I01 - CMP C10 H12 N5 O6 P c1nc(c2c(n....
12 4I0A - CMP C10 H12 N5 O6 P c1nc(c2c(n....
13 4R8H - SP1 C10 H12 N5 O5 P S c1nc(c2c(n....
14 4N9I Kd = 25.6 uM PCG C10 H12 N5 O7 P c1nc2c(n1[....
70% Homology Family (15)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 222 families.
1 4I09 - CMP C10 H12 N5 O6 P c1nc(c2c(n....
2 4HZF - CMP C10 H12 N5 O6 P c1nc(c2c(n....
3 2GZW - CMP C10 H12 N5 O6 P c1nc(c2c(n....
4 4I0B - CMP C10 H12 N5 O6 P c1nc(c2c(n....
5 1HW5 - CMP C10 H12 N5 O6 P c1nc(c2c(n....
6 4FT8 - CMP C10 H12 N5 O6 P c1nc(c2c(n....
7 1I5Z - CMP C10 H12 N5 O6 P c1nc(c2c(n....
8 1G6N - CMP C10 H12 N5 O6 P c1nc(c2c(n....
9 4I02 - CMP C10 H12 N5 O6 P c1nc(c2c(n....
10 1I6X - CMP C10 H12 N5 O6 P c1nc(c2c(n....
11 4I01 - CMP C10 H12 N5 O6 P c1nc(c2c(n....
12 4I0A - CMP C10 H12 N5 O6 P c1nc(c2c(n....
13 4R8H - SP1 C10 H12 N5 O5 P S c1nc(c2c(n....
14 4N9I Kd = 25.6 uM PCG C10 H12 N5 O7 P c1nc2c(n1[....
15 3KCC - CMP C10 H12 N5 O6 P c1nc(c2c(n....
50% Homology Family (15)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 185 families.
1 4I09 - CMP C10 H12 N5 O6 P c1nc(c2c(n....
2 4HZF - CMP C10 H12 N5 O6 P c1nc(c2c(n....
3 2GZW - CMP C10 H12 N5 O6 P c1nc(c2c(n....
4 4I0B - CMP C10 H12 N5 O6 P c1nc(c2c(n....
5 1HW5 - CMP C10 H12 N5 O6 P c1nc(c2c(n....
6 4FT8 - CMP C10 H12 N5 O6 P c1nc(c2c(n....
7 1I5Z - CMP C10 H12 N5 O6 P c1nc(c2c(n....
8 1G6N - CMP C10 H12 N5 O6 P c1nc(c2c(n....
9 4I02 - CMP C10 H12 N5 O6 P c1nc(c2c(n....
10 1I6X - CMP C10 H12 N5 O6 P c1nc(c2c(n....
11 4I01 - CMP C10 H12 N5 O6 P c1nc(c2c(n....
12 4I0A - CMP C10 H12 N5 O6 P c1nc(c2c(n....
13 4R8H - SP1 C10 H12 N5 O5 P S c1nc(c2c(n....
14 4N9I Kd = 25.6 uM PCG C10 H12 N5 O7 P c1nc2c(n1[....
15 3KCC - 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 : 4N9I; Ligand: PCG; 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: 4n9i.bio2) has 45 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
Pocket No.: 2; Query (leader) PDB : 4N9I; Ligand: PCG; Similar sites found: 55
This union binding pocket(no: 2) in the query (biounit: 4n9i.bio2) has 111 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 3RDV ASP SER TRP LYS ASP GLY CYS TYR 0.03573 0.41524 None
2 3THR C2F 0.008993 0.43152 1.42857
3 3PNA CMP 0.000000108 0.71195 1.94805
4 4JWK CTN 0.03492 0.41879 2.59067
5 3HAV ATP 0.01512 0.44088 2.85714
6 1SQS TLA 0.02012 0.42981 2.89256
7 2D6M LBT 0.04305 0.40188 3.14465
8 3SXS PP2 0.01049 0.41837 3.33333
9 2Z9I GLY ALA THR VAL 0.02059 0.43525 3.80952
10 1YKD CMP 0.02572 0.40587 3.80952
11 3ZX4 2M8 0.03738 0.4071 3.861
12 1JZN BGC GAL 0.02129 0.42755 4.44444
13 4Z7X 3CX 0.02188 0.43296 4.7619
14 5M06 ADP 0.0358 0.40483 4.7619
15 5X8I SQZ 0.0372 0.40398 4.7619
16 4X1B MLI 0.02832 0.43658 5.71429
17 5FJJ MAN 0.001371 0.41365 5.71429
18 1ZTH ADP 0.03755 0.41042 5.71429
19 1U5R ATP 0.03287 0.40066 5.74713
20 1DCP HBI 0.01938 0.4371 5.76923
21 2WEI VGG 0.03114 0.40792 5.92335
22 4YMJ 4EJ 0.03595 0.4209 6.19048
23 1GEG GLC 0.03683 0.43013 6.66667
24 3HQP FDP 0.04522 0.40277 6.66667
25 4Q86 AMP 0.01715 0.42107 7.61905
26 1P0Z FLC 0.01619 0.43831 7.63359
27 2OVD DAO 0.02863 0.42768 7.69231
28 4USI AKG 0.03827 0.42186 7.79221
29 5AVF TAU 0.04633 0.40906 8.57143
30 1UZ4 IFL 0.03086 0.42231 9.04762
31 2V7O DRN 0.03555 0.41536 9.04762
32 2R5V HHH 0.02971 0.4123 9.04762
33 4N9Z V3L 0.03056 0.42019 9.52381
34 5C8W PCG 0.00000001944 0.41125 9.79021
35 3W9F I3P 0.02652 0.43332 11.4286
36 4AVB CMP 0.000003114 0.61663 12.381
37 2H8H H8H 0.0108 0.42416 12.381
38 4ZEV M6P 0.03577 0.40485 13.8095
39 4XL8 MNA 0.04005 0.40546 14.3541
40 3SHR CMP 0.0000005352 0.66494 20.9524
41 3OF1 CMP 0.0000007775 0.65644 20.9524
42 3CF6 SP1 0.00002291 0.55899 21.4286
43 5C2N NAG 0.03947 0.41724 22.9167
44 4OFG PCG 0.0000000855 0.69666 27.0833
45 3OCP CMP 0.00000005573 0.71645 28.777
46 5BV6 35G 0.0000002323 0.64117 28.9474
47 4KU7 PCG 0.00000005643 0.70591 29.4118
48 4MUV PCG 0.0000002823 0.65275 30.9859
49 5KJZ PCG 0.000001844 0.61273 31.3333
50 5JAX 6J7 0.0000002768 0.65317 33.3333
51 5H5O PCG 0.0002672 0.51191 36.4341
52 5K8S CMP 0.000000916 0.62017 39.1892
53 2XHK AKG 0.002131 0.48693 44.2857
54 2XKO AKG 0.002763 0.48058 44.2857
55 3LA3 2FT 0.002144 0.48688 45.2381
56 4CYD CMP 0.000009809 0.57708 50
Pocket No.: 3; Query (leader) PDB : 4N9I; Ligand: PCG; Similar sites found: 31
This union binding pocket(no: 3) in the query (biounit: 4n9i.bio1) has 88 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 5F90 GLA GAL 0.0155 0.44653 1.28205
2 4OUC 5ID 0.03383 0.40923 1.90476
3 5XG5 A2G 0.02484 0.43842 2.06897
4 2RC8 DSN 0.02772 0.42884 2.38095
5 4EYG VNL 0.02766 0.4171 2.38095
6 4CS9 AMP 0.03322 0.42719 2.6455
7 1TZD ADP 0.02683 0.43332 2.85714
8 5XQL C2E 0.0452 0.41699 2.85714
9 1YQC GLV 0.01933 0.43386 2.94118
10 1YRO UDP 0.03459 0.4268 3.33333
11 5VCV 1N1 0.02026 0.4004 3.33333
12 2IYF UDP 0.0139 0.44084 3.80952
13 1OT6 HC4 0.04914 0.40394 4
14 4NFN 2KC 0.01656 0.42172 4.28571
15 4XWM CBI 0.04197 0.42169 4.28571
16 1CM8 ANP 0.0434 0.40066 4.28571
17 2B9F ADP 0.03015 0.40566 4.7619
18 5HVJ ANP 0.03502 0.42708 5.2381
19 4Y0X ADP 0.04408 0.40329 5.2381
20 4LH7 1X8 0.0046 0.4721 5.71429
21 2Q4X HMH 0.04603 0.41931 6.19048
22 3IGO ANP 0.02573 0.40073 6.19048
23 5KEW 6SB 0.0461 0.4179 6.38298
24 2VN9 GVD 0.04769 0.41518 8.09524
25 2FQX GMP 0.04174 0.40152 8.57143
26 4LO2 GAL BGC 0.04967 0.40249 8.84354
27 1YYE 196 0.03875 0.40619 9.04762
28 2FR3 REA 0.03296 0.40095 9.48905
29 4JGP PYR 0.04212 0.41894 9.52381
30 4IDT T28 0.04204 0.40136 10.9524
31 4Y8D 49J 0.01861 0.41598 13.3333
Pocket No.: 4; Query (leader) PDB : 4N9I; Ligand: PCG; 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: 4n9i.bio1) has 43 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
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