Receptor
PDB id Resolution Class Description Source Keywords
3N39 2.5 Å EC: 1.17.4.1 RIBONUCLEOTIDE REDUCTASE DIMANGANESE(II)-NRDF FROM ESCHERICH COMPLEX WITH NRDI ESCHERICHIA COLI RIBONUCLEOTIDE REDUCTASE FOUR-HELIX BUNDLE DIMANGANESE CLUFLAVOPROTEIN OXIDOREDUCTASE
Ref.: STRUCTURAL BASIS FOR ACTIVATION OF CLASS IB RIBONUC REDUCTASE. SCIENCE V. 329 1526 2010
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
FMN C:134;
D:134;
Valid;
Valid;
none;
none;
submit data
456.344 C17 H21 N4 O9 P Cc1cc...
MN A:320;
A:321;
B:320;
B:321;
Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
none;
none;
none;
none;
submit data
54.938 Mn [Mn+2...
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90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
3N39 2.5 Å EC: 1.17.4.1 RIBONUCLEOTIDE REDUCTASE DIMANGANESE(II)-NRDF FROM ESCHERICH COMPLEX WITH NRDI ESCHERICHIA COLI RIBONUCLEOTIDE REDUCTASE FOUR-HELIX BUNDLE DIMANGANESE CLUFLAVOPROTEIN OXIDOREDUCTASE
Ref.: STRUCTURAL BASIS FOR ACTIVATION OF CLASS IB RIBONUC REDUCTASE. SCIENCE V. 329 1526 2010
Members (3)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 9 families.
1 3N39 - FMN C17 H21 N4 O9 P Cc1cc2c(cc....
2 3N3A - FMN C17 H21 N4 O9 P Cc1cc2c(cc....
3 3N3B - 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 8 families.
1 3N39 - FMN C17 H21 N4 O9 P Cc1cc2c(cc....
2 3N3A - FMN C17 H21 N4 O9 P Cc1cc2c(cc....
3 3N3B - 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 7 families.
1 3N39 - FMN C17 H21 N4 O9 P Cc1cc2c(cc....
2 3N3A - FMN C17 H21 N4 O9 P Cc1cc2c(cc....
3 3N3B - FMN C17 H21 N4 O9 P Cc1cc2c(cc....
Polypharmacology
Similar Ligands
Ligand no: 1; 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 : 3N39; Ligand: FMN; Similar sites found: 73
This union binding pocket(no: 1) in the query (biounit: 3n39.bio1) has 25 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 4PPF FLC 0.01441 0.42742 2.19436
2 3GFS FMN 0.001272 0.45768 2.87356
3 3DC4 ADP 0.03062 0.40235 3.26797
4 4LTN FMN 0.001939 0.42789 3.5533
5 4LTN NAI 0.002603 0.4155 3.5533
6 5GXU FMN 0.000004087 0.504 3.92157
7 2W5P CL8 0.01932 0.41511 4.02685
8 3QPB R1P 0.0222 0.40154 4.25532
9 5NUL FMN 0.00002999 0.5169 4.34783
10 2PNC CLU 0.03514 0.40242 4.38871
11 3W5J GDP 0.02498 0.41479 4.41176
12 1JJ7 ADP 0.01117 0.43741 4.57516
13 1T5C ADP 0.01676 0.42612 4.57516
14 1B1C FMN 0.000009241 0.53366 5.22876
15 1U1J MET 0.01848 0.40843 5.22876
16 1JS8 MAN MAN BMA 0.005979 0.44686 5.64263
17 2WC1 FMN 0.00000008747 0.62255 5.88235
18 1CZR FMN 0.00000007165 0.56716 5.88235
19 1T5B FMN 0.003768 0.41899 5.88235
20 4KCT FDP 0.01209 0.41062 5.88235
21 2X1L ADN 0.01546 0.40181 5.88235
22 1E5D FMN 0.0001462 0.46301 6.53595
23 1C0I BE2 0.03566 0.41279 6.53595
24 1C0I FAD 0.03566 0.41279 6.53595
25 1GOJ ADP 0.03174 0.41008 6.53595
26 2Z9C FMN 0.001666 0.43073 7
27 2CBZ ATP 0.01721 0.42656 7.173
28 3SVL FMN 0.005816 0.41421 7.77202
29 5K9B FMN 0.000000084 0.62332 7.77778
30 4LPS GDP 0.004766 0.42589 7.84314
31 3IX1 NFM 0.02475 0.4072 8.49673
32 4OXX FMN 0.00000303 0.55493 8.64198
33 1BVY FMN 0.000001671 0.55348 8.77743
34 2AWN ADP 0.01477 0.43319 9.09091
35 1TLL FMN 0.0000185 0.49941 9.15033
36 3TW1 AHN 0.01449 0.42176 9.15033
37 2D2F ADP 0.01318 0.43204 9.2
38 3S2Y FMN 0.0033 0.42152 9.80392
39 2OYS FMN 0.004994 0.40692 9.80392
40 1YQT ADP 0.03183 0.40484 9.80392
41 3VSV XYS 0.03576 0.40055 10.4575
42 3F6R FMN 0.0000001658 0.54528 10.8108
43 5FA6 FAD 0.0002432 0.50329 10.9718
44 5FA6 NAP 0.0002518 0.50329 10.9718
45 5FA6 FMN 0.0002432 0.50329 10.9718
46 3LN9 FLC 0.03188 0.40063 11.5108
47 1G6H ADP 0.01169 0.43584 12.0623
48 1OBV FMN 0.00000005964 0.622 12.4183
49 1T0I FMN 0.001604 0.40417 12.4183
50 1D1Q 4NP 0.03388 0.40025 12.4224
51 3LRE ADP 0.04062 0.40295 13.0719
52 3FJO FMN 0.0000008053 0.5363 13.7255
53 2OHH FMN 0.0002314 0.45897 13.7255
54 4OWK NGA 0.005695 0.42743 13.7681
55 1XPJ TLA 0.04684 0.40711 14.2857
56 2Q9U FMN 0.002533 0.42658 14.3791
57 5A2Z GTP 0.01141 0.42016 14.3791
58 4HEQ FMN 0.0000000395 0.57697 14.3836
59 2XT3 ADP 0.02604 0.41276 14.4201
60 3KAP FMN 0.0000005045 0.57541 14.966
61 4PTZ FMN 0.001632 0.43901 15.6863
62 1D4D SIN 0.02154 0.41035 15.6863
63 1L5J TRA 0.03292 0.40069 15.6863
64 2FCR FMN 0.000000005965 0.58749 16.763
65 4R81 FMN 0.006221 0.4094 16.9935
66 4NAE 1GP 0.03578 0.40138 17.3333
67 4H2D FMN 0.000007747 0.53703 17.5758
68 1AG9 FMN 0.0000001778 0.55371 17.6471
69 3IWD M2T 0.005884 0.43971 20.5882
70 2OG2 MLI 0.01158 0.4319 24.8366
71 3B9Q MLI 0.02653 0.41266 24.8366
72 1AKV FMN 0.0000001799 0.58099 25.1701
73 5LJI FMN 0.00000004011 0.56402 31.7568
Pocket No.: 2; Query (leader) PDB : 3N39; Ligand: FMN; Similar sites found: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 2) in the query (biounit: 3n39.bio1) has 25 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
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