Receptor
PDB id Resolution Class Description Source Keywords
3GFZ 2.05 Å NON-ENZYME: OTHER KLEBSIELLA PNEUMONIAE BLRP1 PH 6 MANGANESE/CY-DIGMP COMPLEX KLEBSIELLA PNEUMONIAE SUBSP. PNEUMONIA78578 TIM-BARREL EAL DOMAIN BLUF DOMAIN HYDROLASE SIGNALING PR
Ref.: STRUCTURE AND MECHANISM OF A BACTERIAL LIGHT-REGULA CYCLIC NUCLEOTIDE PHOSPHODIESTERASE. NATURE V. 459 1015 2009
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
C2E A:501;
B:501;
Valid;
Valid;
none;
none;
submit data
690.411 C20 H24 N10 O14 P2 c1nc2...
FMN A:504;
B:504;
Valid;
Valid;
none;
none;
submit data
456.344 C17 H21 N4 O9 P Cc1cc...
MN A:502;
A:503;
B:502;
B:503;
Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
none;
none;
none;
none;
submit data
54.938 Mn [Mn+2...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
3GFZ 2.05 Å NON-ENZYME: OTHER KLEBSIELLA PNEUMONIAE BLRP1 PH 6 MANGANESE/CY-DIGMP COMPLEX KLEBSIELLA PNEUMONIAE SUBSP. PNEUMONIA78578 TIM-BARREL EAL DOMAIN BLUF DOMAIN HYDROLASE SIGNALING PR
Ref.: STRUCTURE AND MECHANISM OF A BACTERIAL LIGHT-REGULA CYCLIC NUCLEOTIDE PHOSPHODIESTERASE. NATURE V. 459 1015 2009
Members (3)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1256 families.
1 3GG1 - FMN C17 H21 N4 O9 P Cc1cc2c(cc....
2 3GFZ - FMN C17 H21 N4 O9 P Cc1cc2c(cc....
3 3GFX - FMN C17 H21 N4 O9 P Cc1cc2c(cc....
70% Homology Family (3)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1068 families.
1 3GG1 - FMN C17 H21 N4 O9 P Cc1cc2c(cc....
2 3GFZ - FMN C17 H21 N4 O9 P Cc1cc2c(cc....
3 3GFX - FMN C17 H21 N4 O9 P Cc1cc2c(cc....
50% Homology Family (3)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 922 families.
1 3GG1 - FMN C17 H21 N4 O9 P Cc1cc2c(cc....
2 3GFZ - FMN C17 H21 N4 O9 P Cc1cc2c(cc....
3 3GFX - FMN C17 H21 N4 O9 P Cc1cc2c(cc....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: C2E; Similar ligands found: 59
No: Ligand ECFP6 Tc MDL keys Tc
1 PCG 1 0.986111
2 35G 1 0.986111
3 C2E 1 1
4 4BW 0.806818 1
5 1YD 0.806818 1
6 5GP 5GP 0.743902 0.958904
7 4UR 0.731959 1
8 6SW 0.627907 0.944444
9 1YC 0.616162 0.972222
10 6J7 0.58427 0.934211
11 2BA 0.534091 0.916667
12 CMP 0.534091 0.902778
13 GMP 0.53012 0.828947
14 1SY 0.495575 1
15 SGP 0.483871 0.825
16 6SZ 0.483871 0.916667
17 3GP 0.478261 0.92
18 1OR 0.474747 0.741176
19 5GP 0.468085 0.933333
20 G 0.468085 0.933333
21 7CH 0.467391 0.888889
22 6SX 0.462366 0.861111
23 6JR 0.457944 0.944444
24 G2R 0.457143 0.886076
25 GPX 0.451923 0.894737
26 GP3 0.44898 0.947368
27 2GP 0.446809 0.907895
28 GDP BEF 0.445545 0.851852
29 GDP 0.444444 0.921053
30 GP2 0.444444 0.886076
31 GNH 0.44 0.909091
32 P2G 0.4375 0.881579
33 G2P 0.436893 0.886076
34 GDP MG 0.435644 0.873418
35 ALF 5GP 0.431373 0.841463
36 GTP 0.431373 0.921053
37 GMV 0.431373 0.897436
38 G1R 0.427184 0.909091
39 GCP 0.427184 0.897436
40 GNP 0.423077 0.897436
41 GSP 0.423077 0.875
42 G3D 0.423077 0.933333
43 GDP AF3 0.420561 0.841463
44 BEF GDP 0.419048 0.841463
45 GTP MG 0.419048 0.873418
46 GCP G 0.415094 0.884615
47 G4P 0.415094 0.933333
48 GAV 0.415094 0.886076
49 P1G 0.414141 0.87013
50 Y9Z 0.410714 0.833333
51 G G 0.409091 0.934211
52 GDP ALF 0.407407 0.841463
53 N6R 0.40708 0.831169
54 N6S 0.40708 0.831169
55 G3A 0.403509 0.947368
56 YGP 0.401786 0.876543
57 G5P 0.4 0.947368
58 0O2 0.4 0.933333
59 GPG 0.4 0.935065
Ligand no: 2; Ligand: FMN; Similar ligands found: 16
No: Ligand ECFP6 Tc MDL keys Tc
1 FMN 1 1
2 RBF 0.75641 0.876712
3 RS3 0.571429 0.831169
4 FAS 0.543307 0.876543
5 FAD 0.543307 0.876543
6 FAE 0.539062 0.865854
7 DAL FAD PER 0.5 0.833333
8 LFN 0.475 0.643836
9 C3F 0.473684 0.74359
10 CF4 0.463918 0.734177
11 FAY 0.446043 0.864198
12 FNR 0.444444 0.909091
13 RFL 0.442857 0.845238
14 4LS 0.411215 0.875
15 1VY 0.406593 0.769231
16 DLZ 0.404494 0.782051
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 3GFZ; Ligand: FMN; Similar sites found: 65
This union binding pocket(no: 1) in the query (biounit: 3gfz.bio1) has 17 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 3TTM PUT 0.01211 0.41465 1.7341
2 4Y2H SAH 0.01993 0.41773 1.98864
3 2Q2Y ADP 0.01677 0.42061 2.17984
4 2Q2Y MKR 0.01604 0.42061 2.17984
5 5FYR INS 0.01283 0.40134 2.34899
6 3SZB I1E 0.01551 0.40455 2.42131
7 1AUA BOG 0.01563 0.40295 2.7027
8 4DXJ 0M9 0.01311 0.41595 2.76243
9 4DXJ IPE 0.02396 0.40537 2.76243
10 4NZF ARB 0.01341 0.40627 2.90557
11 4A38 BZS 0.01077 0.41456 3.09278
12 3SAO NKN 0.003147 0.41536 3.125
13 4P6X HCY 0.02795 0.40315 3.13725
14 4CQB MLI 0.01131 0.41447 3.1477
15 3BEJ MUF 0.009628 0.41379 3.36134
16 3P7N FMN 0.001088 0.41506 3.48837
17 4QGE 35O 0.00008767 0.40907 3.63196
18 5DXG EST 0.00961 0.40028 3.83142
19 4MG9 27K 0.008137 0.41707 3.92157
20 3EYK EYK 0.01913 0.42389 4.06977
21 1N13 AG2 0.01587 0.40321 4.42478
22 2QQC AG2 0.01521 0.40354 4.46429
23 2WKQ FMN 0.001186 0.41249 4.51807
24 2O5L MNR 0.005405 0.4163 4.57516
25 1XX4 BAM 0.007109 0.419 4.98084
26 1TV5 N8E 0.01765 0.40031 5.08475
27 2Z6C FMN 0.001117 0.41469 5.42636
28 1N9L FMN 0.002053 0.40316 5.50459
29 2BP1 FLC 0.02603 0.40429 5.55556
30 2H12 OAA 0.009446 0.40195 6.2954
31 1XZ3 ICF 0.02672 0.41434 6.32184
32 3RLF MAL 0.009527 0.40897 6.41892
33 3B9Z CO2 0.0352 0.40196 6.4433
34 1SR7 MOF 0.0076 0.4302 6.56371
35 2HHP FLC 0.006393 0.41279 6.77966
36 4ZGM 32M 0.007678 0.42005 7.37705
37 4XCP PLM 0.00619 0.4238 7.64706
38 2PR5 FMN 0.0003586 0.43221 8.33333
39 4MRP GSH 0.02139 0.41676 8.46906
40 3N7S 3N7 0.01708 0.40637 8.69565
41 5OCA 9QZ 0.009911 0.42116 8.73016
42 4A7W GTP 0.02084 0.40573 8.75
43 5CHR 4NC 0.01753 0.40319 8.75912
44 1UO5 PIH 0.006693 0.42893 8.82353
45 1UO4 PIH 0.03065 0.40419 8.82353
46 5H9Q TD2 0.01163 0.41532 9.03226
47 3KP6 SAL 0.01563 0.4005 9.27152
48 4URG C2E 0.01988 0.4007 9.58084
49 3TL1 JRO 0.006007 0.42363 10.6918
50 2Z6D FMN 0.00233 0.40405 10.7692
51 1JGS SAL 0.003881 0.4661 10.8696
52 2P7Q GG6 0.004599 0.42939 11.2782
53 4O4Z N2O 0.03248 0.41003 11.6883
54 4RW3 TDA 0.004543 0.44454 11.9205
55 4RW3 PLM 0.009983 0.42556 11.9205
56 5MBC FMN 0.000000000002268 0.78597 14.4476
57 1NF8 BOG 0.01507 0.41152 15.4589
58 3T50 FMN 0.001233 0.41258 15.625
59 2Y69 CHD 0.01962 0.40754 15.873
60 2HPL ASP ASP LEU TYR GLY 0.01263 0.4116 16
61 4EES FMN 0.0008415 0.41122 23.4783
62 2HFN FMN 0.000000001403 0.65478 35.9477
63 2IYG FMN 0.000000000001852 0.84518 37.9032
64 1YRX FMN 0.00000000003068 0.76289 38.843
65 1X0P FAD 0.00000000005268 0.78357 39.1608
Pocket No.: 2; Query (leader) PDB : 3GFZ; Ligand: C2E; Similar sites found: 23
This union binding pocket(no: 2) in the query (biounit: 3gfz.bio1) has 26 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 5FPE 3TR 0.04122 0.40063 2.06718
2 3GNP SOG 0.005345 0.42514 2.66344
3 1GMN IDS SGN IDS SGN IDS 0.04387 0.40011 2.73224
4 3B0P FMN 0.005795 0.41958 2.85714
5 1VHZ APR 0.04089 0.40086 3.0303
6 1GVF PGH 0.01641 0.41803 3.14685
7 2FJK 13P 0.02281 0.40241 3.27869
8 1TLG GAL 0.01424 0.4309 4
9 3GLC R5P 0.02123 0.40025 4.74576
10 2Q1A 2KT 0.02944 0.40523 4.77816
11 3W9Z FMN 0.009091 0.40369 4.96894
12 2WDB NAG MAN 0.01651 0.42624 5.72917
13 3QDV NDG 0.04049 0.40295 6.99301
14 4NAE 1GP 0.0311 0.40566 8
15 3NZ1 3NY 0.01468 0.42034 8.81226
16 3HCH RSM 0.03311 0.4089 11.6438
17 4LJ3 C2E 0.0000000004755 0.6887 22.2222
18 3HV8 C2E 0.0000000002519 0.72739 25
19 3N3T C2E 0.00000000000494 0.76957 26.3923
20 5MF5 C2E 0.00000000007337 0.71297 26.9531
21 5MKG C2E 0.0000000003601 0.68533 27.1654
22 5M1T C2E 0.0000000000499 0.71967 28.4698
23 3PJU C2E 0.0000000002961 0.66251 30.1205
Pocket No.: 3; Query (leader) PDB : 3GFZ; Ligand: C2E; Similar sites found: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 3) in the query (biounit: 3gfz.bio1) has 26 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
Pocket No.: 4; Query (leader) PDB : 3GFZ; Ligand: FMN; 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: 3gfz.bio1) has 17 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
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