Receptor
PDB id Resolution Class Description Source Keywords
4R8H 1.46 Å NON-ENZYME: TRANSCRIPT_TRANSLATE THE ROLE OF PROTEIN-LIGAND CONTACTS IN ALLOSTERIC REGULATION ESCHERICHIA COLI CATABOLITE ACTIVATOR PROTEIN ESCHERICHIA COLI TRANSCRIPTION FACTOR TRANSCRIPTION
Ref.: THE ROLE OF PROTEIN-LIGAND CONTACTS IN ALLOSTERIC R OF THE ESCHERICHIA COLI CATABOLITE ACTIVATOR PROTEI J.BIOL.CHEM. V. 290 22225 2015
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
SP1 B:302;
B:301;
A:302;
A:301;
Valid;
Valid;
Valid;
Valid;
none;
none;
none;
none;
submit data
345.272 C10 H12 N5 O5 P S c1nc(...
GOL A:304;
B:303;
A:305;
A:303;
A:306;
B:304;
A:307;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
none;
none;
none;
none;
none;
none;
none;
submit data
92.094 C3 H8 O3 C(C(C...
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: SP1; Similar ligands found: 87
No: Ligand ECFP6 Tc MDL keys Tc
1 SP1 1 1
2 RP1 1 1
3 2BA 0.757143 0.915493
4 CMP 0.757143 0.928571
5 1YD 0.580645 0.844156
6 4BW 0.580645 0.844156
7 Y3J 0.542857 0.702703
8 5AD 0.529412 0.722222
9 QQX 0.519481 0.90411
10 XYA 0.514286 0.77027
11 ADN 0.514286 0.77027
12 RAB 0.514286 0.77027
13 5CD 0.513889 0.756757
14 1SY 0.509615 0.844156
15 5N5 0.5 0.746667
16 4UR 0.5 0.844156
17 CC5 0.5 0.791667
18 A4D 0.493151 0.77027
19 MTA 0.480519 0.75
20 75G 0.476744 0.932432
21 EP4 0.473684 0.708861
22 1OR 0.472527 0.759036
23 DTA 0.467532 0.810811
24 M2T 0.467532 0.7125
25 7D7 0.458333 0.72
26 ACK 0.45679 0.835616
27 3AD 0.453333 0.780822
28 SRA 0.451219 0.918919
29 1YC 0.45098 0.818182
30 3DH 0.45 0.75
31 3AM 0.444444 0.851351
32 J7C 0.440476 0.703704
33 ZAS 0.439024 0.721519
34 QQY 0.439024 0.890411
35 AMP 0.439024 0.864865
36 A 0.439024 0.864865
37 6RE 0.433735 0.695122
38 2AM 0.432099 0.84
39 AMP MG 0.428571 0.818182
40 DSH 0.428571 0.703704
41 NEC 0.428571 0.679487
42 A3G 0.428571 0.730769
43 AOC 0.428571 0.75
44 6SX 0.425287 0.885714
45 A2D 0.423529 0.866667
46 A3N 0.423529 0.717949
47 ABM 0.423529 0.842105
48 EEM 0.419355 0.651163
49 S4M 0.418605 0.647727
50 GJV 0.418605 0.686747
51 OVE 0.416667 0.88
52 6SZ 0.41573 0.915493
53 ADX 0.41573 0.82716
54 MAO 0.413793 0.697674
55 7CH 0.413793 0.914286
56 BA3 0.413793 0.866667
57 A3P 0.413793 0.864865
58 AP2 0.413793 0.810127
59 A12 0.413793 0.810127
60 ADP BEF 0.411111 0.7875
61 BEF ADP 0.411111 0.7875
62 5X8 0.411111 0.74026
63 50T 0.411111 0.831169
64 SFG 0.411111 0.705128
65 S7M 0.410526 0.670588
66 5AS 0.409091 0.758621
67 B4P 0.409091 0.866667
68 AP5 0.409091 0.866667
69 ADP 0.409091 0.842105
70 APC 0.406593 0.810127
71 5F1 0.405063 0.688312
72 A3S 0.404494 0.74026
73 SON 0.404494 0.810127
74 A7D 0.404494 0.753247
75 AN2 0.404494 0.831169
76 7D5 0.402439 0.805195
77 AGS 0.402174 0.894737
78 AD9 0.402174 0.820513
79 SAP 0.402174 0.894737
80 SA8 0.402174 0.666667
81 CA0 0.4 0.820513
82 N6R 0.4 0.853333
83 M33 0.4 0.831169
84 ADP MG 0.4 0.807692
85 MHZ 0.4 0.659091
86 AU1 0.4 0.820513
87 N6S 0.4 0.853333
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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