Receptor
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
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
PCG D:301;
A:301;
B:301;
C:301;
Valid;
Valid;
Valid;
Valid;
none;
none;
none;
none;
Kd = 25.6 uM
345.205 C10 H12 N5 O7 P c1nc2...
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: PCG; Similar ligands found: 59
No: Ligand ECFP6 Tc MDL keys Tc
1 PCG 1 1
2 35G 1 1
3 C2E 1 0.986111
4 4BW 0.806818 0.986111
5 1YD 0.806818 0.986111
6 5GP 5GP 0.743902 0.945205
7 4UR 0.731959 0.986111
8 6SW 0.627907 0.957747
9 1YC 0.616162 0.958333
10 6J7 0.58427 0.946667
11 2BA 0.534091 0.902778
12 CMP 0.534091 0.888889
13 GMP 0.53012 0.84
14 1SY 0.495575 0.986111
15 SGP 0.483871 0.835443
16 6SZ 0.483871 0.902778
17 3GP 0.478261 0.932432
18 1OR 0.474747 0.729412
19 5GP 0.468085 0.945946
20 G 0.468085 0.945946
21 7CH 0.467391 0.875
22 6SX 0.462366 0.847222
23 6JR 0.457944 0.930556
24 G2R 0.457143 0.897436
25 GPX 0.451923 0.906667
26 GP3 0.44898 0.934211
27 2GP 0.446809 0.92
28 GDP BEF 0.445545 0.8625
29 GDP 0.444444 0.933333
30 GP2 0.444444 0.897436
31 GNH 0.44 0.921053
32 P2G 0.4375 0.893333
33 G2P 0.436893 0.897436
34 GDP MG 0.435644 0.884615
35 ALF 5GP 0.431373 0.851852
36 GTP 0.431373 0.933333
37 GMV 0.431373 0.909091
38 G1R 0.427184 0.921053
39 GCP 0.427184 0.909091
40 GNP 0.423077 0.909091
41 GSP 0.423077 0.886076
42 G3D 0.423077 0.945946
43 GDP AF3 0.420561 0.851852
44 BEF GDP 0.419048 0.851852
45 GTP MG 0.419048 0.884615
46 GCP G 0.415094 0.896104
47 G4P 0.415094 0.945946
48 GAV 0.415094 0.897436
49 P1G 0.414141 0.881579
50 Y9Z 0.410714 0.843373
51 G G 0.409091 0.921053
52 GDP ALF 0.407407 0.851852
53 N6R 0.40708 0.818182
54 N6S 0.40708 0.818182
55 G3A 0.403509 0.934211
56 YGP 0.401786 0.8875
57 G5P 0.4 0.934211
58 0O2 0.4 0.945946
59 GPG 0.4 0.922078
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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