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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 291 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 247 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 209 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: 85
No: Ligand ECFP6 Tc MDL keys Tc
1 RP1 1 1
2 SP1 1 1
3 CMP 0.757143 0.928571
4 2BA 0.757143 0.915493
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 RAB 0.514286 0.77027
11 ADN 0.514286 0.77027
12 XYA 0.514286 0.77027
13 5CD 0.513889 0.756757
14 1SY 0.509615 0.844156
15 CC5 0.5 0.791667
16 4UR 0.5 0.844156
17 5N5 0.5 0.746667
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 M2T 0.467532 0.7125
24 DTA 0.467532 0.810811
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 AMP 0.439024 0.864865
34 A 0.439024 0.864865
35 LMS 0.439024 0.804878
36 ZAS 0.439024 0.721519
37 QQY 0.439024 0.890411
38 6RE 0.433735 0.695122
39 2AM 0.432099 0.84
40 NEC 0.428571 0.679487
41 AOC 0.428571 0.75
42 DSH 0.428571 0.703704
43 A3G 0.428571 0.730769
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 GJV 0.418605 0.686747
50 S4M 0.418605 0.647727
51 OVE 0.416667 0.88
52 6SZ 0.41573 0.915493
53 ADX 0.41573 0.82716
54 7CH 0.413793 0.914286
55 A12 0.413793 0.810127
56 A3P 0.413793 0.864865
57 BA3 0.413793 0.866667
58 AP2 0.413793 0.810127
59 MAO 0.413793 0.697674
60 SFG 0.411111 0.705128
61 50T 0.411111 0.831169
62 5X8 0.411111 0.74026
63 S7M 0.410526 0.670588
64 AP5 0.409091 0.866667
65 5AS 0.409091 0.758621
66 ADP 0.409091 0.842105
67 B4P 0.409091 0.866667
68 APC 0.406593 0.810127
69 5F1 0.405063 0.688312
70 AT4 0.404494 0.881579
71 SON 0.404494 0.810127
72 A3S 0.404494 0.74026
73 A7D 0.404494 0.753247
74 AN2 0.404494 0.831169
75 7D5 0.402439 0.805195
76 AD9 0.402174 0.820513
77 SA8 0.402174 0.666667
78 SAP 0.402174 0.894737
79 AGS 0.402174 0.894737
80 AU1 0.4 0.820513
81 N6R 0.4 0.853333
82 CA0 0.4 0.820513
83 MHZ 0.4 0.659091
84 N6S 0.4 0.853333
85 M33 0.4 0.831169
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 4N9I; Ligand: PCG; Similar sites found with APoc: 107
This union binding pocket(no: 1) in the query (biounit: 4n9i.bio2) has 45 residues
No: Leader PDB Ligand Sequence Similarity
1 2YIP YIO None
2 3THR C2F 1.42857
3 5O0J GLC 1.90476
4 3PNA CMP 1.94805
5 1VJY 460 2.38095
6 5JFS 6K0 2.38095
7 3PTG 932 2.38095
8 3HAV ATP 2.85714
9 4Z1D PEP 2.85714
10 1OFZ FUL 2.85714
11 1OFZ FUC 2.85714
12 5IFK HPA 2.85714
13 3MQG ACO 3.125
14 2D6M LBT 3.14465
15 4P86 5GP 3.27869
16 5VCV 1N1 3.33333
17 5HCY 60D 3.33333
18 2XZ9 PYR 3.33333
19 4OJP MAL 3.33333
20 5W3K NDP 3.33333
21 5W3K 9TY 3.33333
22 2GU8 796 3.33333
23 1RJW ETF 3.80952
24 2OFV 242 3.80952
25 1I7L ATP 3.80952
26 6HL7 CP 4.28571
27 5ZI9 FLC 4.28571
28 5E58 CPZ 4.28571
29 2Q37 3AL 4.41989
30 1JZN BGC GAL 4.44444
31 4Z7X 3CX 4.7619
32 5JGA 6KC 4.7619
33 4XV1 904 4.7619
34 5M06 ADP 4.7619
35 5K2M ADP 4.7619
36 4LOO SB4 4.7619
37 3A76 SPD 5.11364
38 1IT7 GUN 5.2381
39 5HVJ ANP 5.2381
40 4OB6 S2T 5.2381
41 4X1B MLI 5.71429
42 5N87 N66 5.71429
43 5MB4 NDG 5.71429
44 1ZTH ADP 5.71429
45 1DCP HBI 5.76923
46 2WEI VGG 5.92335
47 6D61 4AA 6.19048
48 5CKS GAL 6.19048
49 4YMJ 4EJ 6.19048
50 2J5V PCA 6.19048
51 4YSX MLI 6.19048
52 5KEW 6SB 6.38298
53 5E5U MLT 6.53266
54 3E8N ATP 6.66667
55 3E8N VRA 6.66667
56 4NW6 2NS 6.66667
57 2HFK E4H 6.66667
58 4MUQ LY0 6.66667
59 5O5Y GLC 6.66667
60 3O7J 2AL 6.87831
61 1RRC ADP 7.14286
62 1M3U KPL 7.14286
63 4C2V YJA 7.61905
64 5EYK 5U5 7.61905
65 4Q86 AMP 7.61905
66 5HSS 64Z 7.61905
67 6CGZ HL6 7.61905
68 5Y80 IRE 8.09524
69 3LXK MI1 8.09524
70 3C3N FMN 8.57143
71 2GMP NAG MAN 8.57143
72 4ISS TAR 8.57143
73 1UZ4 IFL 9.04762
74 2V7O DRN 9.04762
75 4KBA 1QM 9.04762
76 5C8W PCG 9.79021
77 2IMP LAC 10
78 2BO4 FLC 10.4762
79 1I7A PHE 10.8108
80 5DEY 59T 10.9524
81 4U00 ADP 10.9524
82 4AVB CMP 12.381
83 4H4D 10E 13.8095
84 1O68 KIV 13.8095
85 1N1G BCP 13.8095
86 5T7I LAT NAG GAL 15.4839
87 1CX4 CMP 19.0476
88 3NW7 LGV 19.5238
89 3OF1 CMP 20.9524
90 3SHR CMP 20.9524
91 3CF6 SP1 21.4286
92 1NE6 SP1 22.381
93 4NVP 7CH 22.9665
94 4N14 WR7 25.7143
95 4OFG PCG 27.0833
96 5KBF CMP 27.619
97 3OCP CMP 28.777
98 5BV6 35G 28.9474
99 4KU7 PCG 29.4118
100 4MUV PCG 30.9859
101 5KJZ PCG 31.3333
102 5JAX 6J7 33.3333
103 5H5O PCG 36.4341
104 5K8S CMP 39.1892
105 2XKO AKG 44.2857
106 2XHK AKG 44.2857
107 3LA3 2FT 45.2381
108 4CYD CMP 50
Pocket No.: 2; Query (leader) PDB : 4N9I; Ligand: PCG; Similar sites found with APoc: 42
This union binding pocket(no: 2) in the query (biounit: 4n9i.bio2) has 111 residues
No: Leader PDB Ligand Sequence Similarity
1 3RDV ASP SER TRP LYS ASP GLY CYS TYR None
2 6B9R 2HE 2.38095
3 4JWK CTN 2.59067
4 3DAK ANP 2.85714
5 1SQS TLA 2.89256
6 3B9Z CO2 3.33333
7 3SXS PP2 3.33333
8 2Z9I GLY ALA THR VAL 3.80952
9 1YKD CMP 3.80952
10 3ZX4 2M8 3.861
11 3NOJ PYR 4.20168
12 1TL2 NDG 4.7619
13 1Q19 SSC 4.7619
14 3TXO 07U 4.7619
15 3I7S PYR 4.7619
16 4A05 CBI 5.2381
17 5FJJ MAN 5.71429
18 1U5R ATP 5.74713
19 2X2M X2M 6.19048
20 5IXB LGA 6.48148
21 1GEG GLC 6.66667
22 3HQP FDP 6.66667
23 1P0Z FLC 7.63359
24 2OVD DAO 7.69231
25 4USI AKG 7.79221
26 5AVF TAU 8.57143
27 6F3G CJN 9.04762
28 2R5V HHH 9.04762
29 5Z84 CHD 10.8696
30 5ZCO PGV 10.8696
31 5W97 CHD 10.8696
32 2DYR PGV 10.8696
33 5Z84 PGV 10.8696
34 4IDT T28 10.9524
35 3W9F I3P 11.4286
36 4W6Z ETF 11.4286
37 6B9T 2HE 11.9048
38 2H8H H8H 12.381
39 4ZEV M6P 13.8095
40 3KPE TM3 17.6471
41 5C2N NAG 22.9167
42 5NNT DPV 48.6486
Pocket No.: 3; Query (leader) PDB : 4N9I; Ligand: PCG; Similar sites found with APoc: 58
This union binding pocket(no: 3) in the query (biounit: 4n9i.bio1) has 88 residues
No: Leader PDB Ligand Sequence Similarity
1 5F90 GLA GAL 1.28205
2 4OUC 5ID 1.90476
3 5XG5 A2G 2.06897
4 2RC8 DSN 2.38095
5 4EYG VNL 2.38095
6 4CS9 AMP 2.6455
7 1TZD ADP 2.85714
8 5XQL C2E 2.85714
9 2XOC ADP 2.85714
10 1YQC GLV 2.94118
11 5YLF BGC 3.33333
12 5GQX GLC GLC GLC GLC 3.33333
13 5NM7 GLY 3.33333
14 1YRO UDP 3.33333
15 3PN1 IVH 3.33333
16 1DKU AP2 3.33333
17 6E8I PTR 3.5503
18 2IYF UDP 3.80952
19 3KLL MAL 3.80952
20 3FSY SCA 3.80952
21 4CJN MUR 3.80952
22 1OT6 HC4 4
23 4QM7 GTP 4.09357
24 4NFN 2KC 4.28571
25 4XWM CBI 4.28571
26 5NDB 8TW 4.28571
27 1CM8 ANP 4.28571
28 2TOH HBI 4.7619
29 2B9F ADP 4.7619
30 5A96 GTP 5.2381
31 4TV1 36M 5.2381
32 5QIN J2V 5.2381
33 4Y0X ADP 5.2381
34 4LH7 1X8 5.71429
35 2BMB PMM 6.19048
36 1O9U ADZ 6.19048
37 2Q4X HMH 6.19048
38 3IGO ANP 6.19048
39 5IDB BMA 6.33803
40 1OGD RIP 6.87023
41 4G86 BNT 7.61905
42 6AC9 ANP 7.61905
43 4C2W ANP 7.61905
44 2Z49 AMG 8.09524
45 2VN9 GVD 8.09524
46 6BJ0 G6P 8.57143
47 2FQX GMP 8.57143
48 4LO2 GAL BGC 8.84354
49 1YYE 196 9.04762
50 2FR3 REA 9.48905
51 4JGP PYR 9.52381
52 4OAV ACP 9.52381
53 3K5I AIR 10.9524
54 5ME4 HP4 10.9524
55 4Y8D 49J 13.3333
56 6G47 SIA 14.3541
57 6CB2 OLC 18.43
58 4V1T ADP 20.3125
Pocket No.: 4; Query (leader) PDB : 4N9I; Ligand: PCG; Similar sites found with APoc: 51
This union binding pocket(no: 4) in the query (biounit: 4n9i.bio1) has 43 residues
No: Leader PDB Ligand Sequence Similarity
1 5YRL GLC GLC None
2 3CYI ATP None
3 4R29 SAM 1.42857
4 5UR1 YY9 2.38095
5 4OOE FOM 2.38095
6 3ISN EDM 2.85714
7 3EUF BAU 2.85714
8 4P5Z Q7M 2.85714
9 3WXL ADP 2.85714
10 5DRB 5FJ 2.85714
11 4EWH T77 3.33333
12 2D2F ADP 3.33333
13 2UVO NAG 3.50877
14 4GJ3 0XP 3.80952
15 1H5R G1P 3.80952
16 4CJN QNZ 3.80952
17 2CHT TSA 3.93701
18 2DT9 THR 4.19162
19 5YRJ BGC GLC 4.22535
20 4G31 0WH 4.28571
21 4N6H EJ4 4.28571
22 3KDM TES 4.7619
23 2O66 FLC 5.18518
24 3O03 GCO 5.2381
25 1SDW IYT 5.2381
26 5V3D FCN 5.51724
27 2Q6B HR2 5.71429
28 3BJE URA 5.71429
29 3C0G 3AM 6.19048
30 1Q11 TYE 6.19048
31 3BGD PM6 6.19048
32 1Q8Y ADE 6.19048
33 5EW9 5VC 6.19048
34 3KB6 LAC 6.19048
35 5A7C 5D4 6.19469
36 5JSP DQY 6.46766
37 1T9D P22 7.14286
38 3UNG ADP 7.14286
39 5HSS 650 7.61905
40 3AB4 THR 7.61905
41 2HJR CIT 8.57143
42 4JX1 CAH 8.84956
43 3HZT J60 9.04762
44 1V0O INR 9.52381
45 4RYV ZEA 9.67742
46 1UA4 GLC 10.4762
47 1UA4 BGC 10.4762
48 6F5W KG1 12.381
49 4FGC PQ0 13.3333
50 4P7U 1PS 17.8571
51 3FYP PEP 19.5238
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