Receptor
PDB id Resolution Class Description Source Keywords
2ABA 1.05 Å EC: 1.6.99.1 STRUCTURE OF REDUCED PETN REDUCTASE IN COMPLEX WITH PROGESTERONE ENTEROBACTER CLOACAE REDUCED FLAVOPROTEIN ATOMIC RESOLUTION PROGESTERONE PETNOXIDOREDUCTASE
Ref.: PROTON TRANSFER IN THE OXIDATIVE HALF-REACTION OF PENTAERYTHRITOL TETRANITRATE REDUCTASE FEBS J. V. 272 4660 2005
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
FMN A:1401;
 Valid;
 none;
 submit data
456.344 C17 H21 N4 O9 P Cc1cc...
IPA A:1501;
A:1502;
 Valid;
Valid;
 none;
none;
 submit data
60.095 C3 H8 O CC(C)...
STR A:1500;
 Valid;
 none;
 Kd = 0.7 uM
314.462 C21 H30 O2 CC(=O...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
1VYP 1.27 Å EC: 1.6.99.1 STRUCTURE OF PENTAERYTHRITOL TETRANITRATE REDUCTASE W102F MU COMPLEXED WITH PICRIC ACID ENTEROBACTER CLOACAE OXIDOREDUCTASE FLAVOENZYME EXPLOSIVE DEGRADATION STEROID
Ref.: ATOMIC RESOLUTION STRUCTURES AND SOLUTION BEHAVIOR ENZYME-SUBSTRATE COMPLEXES OF ENTEROBACTER CLOACAE PENTAERYTHRITOL TETRANITRATE REDUCTASE: MULTIPLE CONFORMATIONAL STATES AND IMPLICATIONS FOR THE MECH NITROAROMATIC EXPLOSIVE DEGRADATION J.BIOL.CHEM
Members (29)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 8 families.
1 1H60 Kd = 20 uM STR C21 H30 O2 CC(=O)[C@H....
2 3P7Y - P7Y C8 H7 N O3 c1ccc(c(c1....
3 1H50 - FMN C17 H21 N4 O9 P Cc1cc2c(cc....
4 3P67 - FMN C17 H21 N4 O9 P Cc1cc2c(cc....
5 3KFT - NAD C21 H27 N7 O14 P2 c1cc(c[n+]....
6 1VYP Kd = 0.07 uM TNF C6 H3 N3 O7 c1c(cc(c(c....
7 3P74 - FMN C17 H21 N4 O9 P Cc1cc2c(cc....
8 1GVQ - A2Q C6 H8 O C1CC=CC(=O....
9 5LGX - FMN C17 H21 N4 O9 P Cc1cc2c(cc....
10 2ABA Kd = 0.7 uM STR C21 H30 O2 CC(=O)[C@H....
11 6GIA - FMN C17 H21 N4 O9 P Cc1cc2c(cc....
12 6GI7 - FMN C17 H21 N4 O9 P Cc1cc2c(cc....
13 1VYS Kd = 0.24 uM TNF C6 H3 N3 O7 c1c(cc(c(c....
14 1GVO - FMN C17 H21 N4 O9 P Cc1cc2c(cc....
15 3P81 - P81 C8 H7 N O3 c1cc(ccc1/....
16 5LGZ - FNR C17 H23 N4 O9 P Cc1cc2c(cc....
17 3P62 - FMN C17 H21 N4 O9 P Cc1cc2c(cc....
18 6GI9 - FMN C17 H21 N4 O9 P Cc1cc2c(cc....
19 3P82 - FMN C17 H21 N4 O9 P Cc1cc2c(cc....
20 1GVR - TNL C7 H5 N3 O6 Cc1c(cc(cc....
21 1H63 - FMN C17 H21 N4 O9 P Cc1cc2c(cc....
22 1H62 Kd = 17 uM ANB C19 H24 O2 C[C@]12CC[....
23 1GVS - TNF C6 H3 N3 O7 c1c(cc(c(c....
24 1H61 Kd = 13 uM PDN C21 H26 O5 C[C@]12CC(....
25 3P80 - P80 C8 H7 N O3 c1cc(cc(c1....
26 2ABB - IPA C3 H8 O CC(C)O
27 6GI8 - FMN C17 H21 N4 O9 P Cc1cc2c(cc....
28 1VYR Kd = 5.4 uM TNF C6 H3 N3 O7 c1c(cc(c(c....
29 1H51 - FMN C17 H21 N4 O9 P Cc1cc2c(cc....
70% Homology Family (29)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 6 families.
1 1H60 Kd = 20 uM STR C21 H30 O2 CC(=O)[C@H....
2 3P7Y - P7Y C8 H7 N O3 c1ccc(c(c1....
3 1H50 - FMN C17 H21 N4 O9 P Cc1cc2c(cc....
4 3P67 - FMN C17 H21 N4 O9 P Cc1cc2c(cc....
5 3KFT - NAD C21 H27 N7 O14 P2 c1cc(c[n+]....
6 1VYP Kd = 0.07 uM TNF C6 H3 N3 O7 c1c(cc(c(c....
7 3P74 - FMN C17 H21 N4 O9 P Cc1cc2c(cc....
8 1GVQ - A2Q C6 H8 O C1CC=CC(=O....
9 5LGX - FMN C17 H21 N4 O9 P Cc1cc2c(cc....
10 2ABA Kd = 0.7 uM STR C21 H30 O2 CC(=O)[C@H....
11 6GIA - FMN C17 H21 N4 O9 P Cc1cc2c(cc....
12 6GI7 - FMN C17 H21 N4 O9 P Cc1cc2c(cc....
13 1VYS Kd = 0.24 uM TNF C6 H3 N3 O7 c1c(cc(c(c....
14 1GVO - FMN C17 H21 N4 O9 P Cc1cc2c(cc....
15 3P81 - P81 C8 H7 N O3 c1cc(ccc1/....
16 5LGZ - FNR C17 H23 N4 O9 P Cc1cc2c(cc....
17 3P62 - FMN C17 H21 N4 O9 P Cc1cc2c(cc....
18 6GI9 - FMN C17 H21 N4 O9 P Cc1cc2c(cc....
19 3P82 - FMN C17 H21 N4 O9 P Cc1cc2c(cc....
20 1GVR - TNL C7 H5 N3 O6 Cc1c(cc(cc....
21 1H63 - FMN C17 H21 N4 O9 P Cc1cc2c(cc....
22 1H62 Kd = 17 uM ANB C19 H24 O2 C[C@]12CC[....
23 1GVS - TNF C6 H3 N3 O7 c1c(cc(c(c....
24 1H61 Kd = 13 uM PDN C21 H26 O5 C[C@]12CC(....
25 3P80 - P80 C8 H7 N O3 c1cc(cc(c1....
26 2ABB - IPA C3 H8 O CC(C)O
27 6GI8 - FMN C17 H21 N4 O9 P Cc1cc2c(cc....
28 1VYR Kd = 5.4 uM TNF C6 H3 N3 O7 c1c(cc(c(c....
29 1H51 - FMN C17 H21 N4 O9 P Cc1cc2c(cc....
50% Homology Family (75)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 2 families.
1 1H60 Kd = 20 uM STR C21 H30 O2 CC(=O)[C@H....
2 3P7Y - P7Y C8 H7 N O3 c1ccc(c(c1....
3 1H50 - FMN C17 H21 N4 O9 P Cc1cc2c(cc....
4 3P67 - FMN C17 H21 N4 O9 P Cc1cc2c(cc....
5 3KFT - NAD C21 H27 N7 O14 P2 c1cc(c[n+]....
6 1VYP Kd = 0.07 uM TNF C6 H3 N3 O7 c1c(cc(c(c....
7 3P74 - FMN C17 H21 N4 O9 P Cc1cc2c(cc....
8 1GVQ - A2Q C6 H8 O C1CC=CC(=O....
9 5LGX - FMN C17 H21 N4 O9 P Cc1cc2c(cc....
10 2ABA Kd = 0.7 uM STR C21 H30 O2 CC(=O)[C@H....
11 6GIA - FMN C17 H21 N4 O9 P Cc1cc2c(cc....
12 6GI7 - FMN C17 H21 N4 O9 P Cc1cc2c(cc....
13 1VYS Kd = 0.24 uM TNF C6 H3 N3 O7 c1c(cc(c(c....
14 1GVO - FMN C17 H21 N4 O9 P Cc1cc2c(cc....
15 3P81 - P81 C8 H7 N O3 c1cc(ccc1/....
16 5LGZ - FNR C17 H23 N4 O9 P Cc1cc2c(cc....
17 3P62 - FMN C17 H21 N4 O9 P Cc1cc2c(cc....
18 6GI9 - FMN C17 H21 N4 O9 P Cc1cc2c(cc....
19 3P82 - FMN C17 H21 N4 O9 P Cc1cc2c(cc....
20 1GVR - TNL C7 H5 N3 O6 Cc1c(cc(cc....
21 1H63 - FMN C17 H21 N4 O9 P Cc1cc2c(cc....
22 1H62 Kd = 17 uM ANB C19 H24 O2 C[C@]12CC[....
23 1GVS - TNF C6 H3 N3 O7 c1c(cc(c(c....
24 1H61 Kd = 13 uM PDN C21 H26 O5 C[C@]12CC(....
25 3P80 - P80 C8 H7 N O3 c1cc(cc(c1....
26 2ABB - IPA C3 H8 O CC(C)O
27 6GI8 - FMN C17 H21 N4 O9 P Cc1cc2c(cc....
28 1VYR Kd = 5.4 uM TNF C6 H3 N3 O7 c1c(cc(c(c....
29 1H51 - FMN C17 H21 N4 O9 P Cc1cc2c(cc....
30 2GQ9 - HBA C7 H6 O2 c1cc(ccc1C....
31 2GQ8 - FMN C17 H21 N4 O9 P Cc1cc2c(cc....
32 2GOU - FMN C17 H21 N4 O9 P Cc1cc2c(cc....
33 2GQA - FMN C17 H21 N4 O9 P Cc1cc2c(cc....
34 2HS8 - FMN C17 H21 N4 O9 P Cc1cc2c(cc....
35 2HS6 - FMN C17 H21 N4 O9 P Cc1cc2c(cc....
36 3HGO - FMN C17 H21 N4 O9 P Cc1cc2c(cc....
37 2HSA - FMN C17 H21 N4 O9 P Cc1cc2c(cc....
38 3HGS - PHB C7 H6 O3 c1cc(ccc1C....
39 1OYB - HBA C7 H6 O2 c1cc(ccc1C....
40 1OYC - FMN C17 H21 N4 O9 P Cc1cc2c(cc....
41 1BWK - FMN C17 H21 N4 O9 P Cc1cc2c(cc....
42 1OYA - FMN C17 H21 N4 O9 P Cc1cc2c(cc....
43 6AGZ - FMN C17 H21 N4 O9 P Cc1cc2c(cc....
44 4M5P - MLA C3 H4 O4 C(C(=O)O)C....
45 4TMB - FMN C17 H21 N4 O9 P Cc1cc2c(cc....
46 4TMC - FMN C17 H21 N4 O9 P Cc1cc2c(cc....
47 6S32 - BAM C7 H9 N2 c1ccc(cc1)....
48 1ICS - FMN C17 H21 N4 O9 P Cc1cc2c(cc....
49 3HGR - PHB C7 H6 O3 c1cc(ccc1C....
50 1ICP - FMN C17 H21 N4 O9 P Cc1cc2c(cc....
51 1ICQ - OPD C18 H28 O3 CCC=CC[C@@....
52 3ATY - FMN C17 H21 N4 O9 P Cc1cc2c(cc....
53 3ATZ - HBA C7 H6 O2 c1cc(ccc1C....
54 6UFF - FMN C17 H21 N4 O9 P Cc1cc2c(cc....
55 6MYW - FMN C17 H21 N4 O9 P Cc1cc2c(cc....
56 6O08 - FMN C17 H21 N4 O9 P Cc1cc2c(cc....
57 1Q45 - FMN C17 H21 N4 O9 P Cc1cc2c(cc....
58 2Q3O - FMN C17 H21 N4 O9 P Cc1cc2c(cc....
59 2R14 Kd = 0.63 mM TXD C21 H31 N7 O14 P2 c1nc(c2c(n....
60 3GX9 - TXD C21 H31 N7 O14 P2 c1nc(c2c(n....
61 1GWJ - FMN C17 H21 N4 O9 P Cc1cc2c(cc....
62 1VJI - FMN C17 H21 N4 O9 P Cc1cc2c(cc....
63 2Q3R - FMN C17 H21 N4 O9 P Cc1cc2c(cc....
64 4JIQ Kd = 0.73 mM 1L5 C9 H9 N O2 C/C(=CN(=O....
65 4JIP - HBA C7 H6 O2 c1cc(ccc1C....
66 4JIC - FMN C17 H21 N4 O9 P Cc1cc2c(cc....
67 5N6G - FMN C17 H21 N4 O9 P Cc1cc2c(cc....
68 4QNW - FMN C17 H21 N4 O9 P Cc1cc2c(cc....
69 6S31 - FMN C17 H21 N4 O9 P Cc1cc2c(cc....
70 6S23 - KSW C6 H6 O CC1=CC=CC1....
71 6S0G - FMN C17 H21 N4 O9 P Cc1cc2c(cc....
72 4RNX - FMN C17 H21 N4 O9 P Cc1cc2c(cc....
73 4RNV - FMN C17 H21 N4 O9 P Cc1cc2c(cc....
74 4RNW - FMN C17 H21 N4 O9 P Cc1cc2c(cc....
75 4A3U - FMN C17 H21 N4 O9 P Cc1cc2c(cc....
Polypharmacology
Similar Ligands (2D)
Ligand no: 1; Ligand: FMN; Similar ligands found: 18
No: Ligand ECFP6 Tc MDL keys Tc
1 FMN 1 1
2 RBF 0.75641 0.876712
3 9O9 0.574468 0.934211
4 RS3 0.571429 0.831169
5 FAD 0.543307 0.876543
6 FAS 0.543307 0.876543
7 FAE 0.539062 0.865854
8 UBG 0.534351 0.888889
9 5DD 0.475248 0.972603
10 LFN 0.475 0.643836
11 C3F 0.473684 0.74359
12 CF4 0.463918 0.734177
13 FAY 0.446043 0.864198
14 FNR 0.444444 0.909091
15 RFL 0.442857 0.845238
16 4LS 0.411215 0.875
17 1VY 0.406593 0.769231
18 DLZ 0.404494 0.782051
Ligand no: 2; Ligand: IPA; Similar ligands found: 1
No: Ligand ECFP6 Tc MDL keys Tc
1 IPA 1 1
Ligand no: 3; Ligand: STR; Similar ligands found: 12
No: Ligand ECFP6 Tc MDL keys Tc
1 STR 1 1
2 1CA 0.732394 0.775
3 FFA 0.619718 0.833333
4 TES 0.619718 0.833333
5 3G6 0.618421 0.861111
6 TH2 0.554217 0.775
7 K2B 0.542169 0.852941
8 DL4 0.54023 0.794872
9 ASD 0.520548 1
10 PLO 0.433735 0.857143
11 CI2 0.419753 0.870968
12 C0R 0.411111 0.738095
Similar Ligands (3D)
Ligand no: 1; Ligand: FMN; Similar ligands found: 10
No: Ligand Similarity coefficient
1 7O6 0.9670
2 4X4 0.8996
3 4LU 0.8884
4 E2U 0.8865
5 HDF 0.8834
6 AFQ 0.8817
7 E2X 0.8805
8 E89 0.8698
9 1WJ 0.8673
10 FZZ 0.8606
Ligand no: 2; Ligand: IPA; Similar ligands found: 68
No: Ligand Similarity coefficient
1 BEF 1.0000
2 2PO 1.0000
3 78T 1.0000
4 AF3 1.0000
5 ACM 0.9910
6 SEY 0.9900
7 KCS 0.9870
8 ACT 0.9860
9 VN4 0.9819
10 FAH 0.9618
11 MCH 0.9612
12 GOA 0.9545
13 2A3 0.9532
14 PPI 0.9496
15 GLV 0.9363
16 HAE 0.9356
17 GLY 0.9348
18 NIE 0.9340
19 F50 0.9339
20 ALA 0.9329
21 TBU 0.9294
22 03S 0.9294
23 TMO 0.9285
24 F3V 0.9278
25 R3W 0.9273
26 TSZ 0.9272
27 2A1 0.9258
28 HVB 0.9255
29 2HP 0.9224
30 GB 0.9196
31 AKR 0.9187
32 61G 0.9180
33 FPO 0.9176
34 J3K 0.9171
35 MGX 0.9170
36 AGU 0.9140
37 CP2 0.9127
38 PO4 0.9111
39 BF4 0.9110
40 NHY 0.9100
41 BRJ 0.9094
42 NMU 0.9080
43 2PA 0.9077
44 ATO 0.9070
45 BRP 0.9049
46 1BP 0.9045
47 EDO 0.9027
48 BXA 0.9021
49 ART 0.9021
50 FUS 0.9000
51 PEJ 0.8974
52 WO6 0.8968
53 TCV 0.8930
54 IMD 0.8930
55 HUH 0.8930
56 ALF 0.8921
57 PZO 0.8920
58 NOE 0.8914
59 SO2 0.8910
60 OSM 0.8894
61 GXV 0.8860
62 TRI 0.8860
63 9XN 0.8836
64 HP4 0.8830
65 MSM 0.8790
66 GOL 0.8730
67 3GR 0.8654
68 AXO 0.8620
Ligand no: 3; Ligand: STR; Similar ligands found: 103
No: Ligand Similarity coefficient
1 DHT 0.9621
2 PDN 0.9596
3 HCY 0.9594
4 AOM 0.9540
5 5SD 0.9519
6 AND 0.9513
7 AOX 0.9499
8 AS4 0.9488
9 ANB 0.9467
10 TUA 0.9445
11 ZK5 0.9409
12 AOI 0.9399
13 BDT 0.9382
14 6VW 0.9353
15 ANO 0.9331
16 TUV 0.9321
17 DEX 0.9283
18 R18 0.9248
19 ESR 0.9225
20 NQ8 0.9195
21 AON 0.9178
22 17M 0.9168
23 EST 0.9155
24 NDR 0.9144
25 30Q 0.9057
26 CUE 0.9047
27 EQU 0.9045
28 AO 0.9032
29 801 0.8989
30 120 0.8988
31 CR4 0.8983
32 MBT 0.8980
33 BMZ 0.8962
34 J3Z 0.8941
35 SAU 0.8928
36 124 0.8923
37 ESZ 0.8905
38 NOG 0.8868
39 17H 0.8867
40 FIT 0.8866
41 GEN 0.8859
42 802 0.8841
43 ESL 0.8838
44 1N7 0.8830
45 END 0.8825
46 1DR 0.8812
47 EES 0.8794
48 ECS 0.8782
49 789 0.8780
50 18E 0.8776
51 272 0.8771
52 BBP 0.8764
53 397 0.8751
54 797 0.8749
55 A05 0.8745
56 SDN 0.8741
57 BER 0.8741
58 AQN 0.8736
59 609 0.8707
60 122 0.8704
61 A63 0.8683
62 BRZ 0.8681
63 3WF 0.8681
64 6ZE 0.8668
65 1UR 0.8666
66 5OR 0.8663
67 517 0.8658
68 97K 0.8654
69 27F 0.8653
70 79X 0.8644
71 TUS 0.8640
72 Q0K 0.8638
73 KMP 0.8636
74 907 0.8631
75 1UT 0.8631
76 08C 0.8630
77 334 0.8628
78 20D 0.8627
79 1V0 0.8625
80 A64 0.8625
81 SLX 0.8625
82 1UZ 0.8621
83 ADL 0.8615
84 BRY 0.8613
85 47X 0.8607
86 ESM 0.8607
87 29F 0.8601
88 IXM 0.8598
89 WG8 0.8591
90 DX7 0.8576
91 SNL 0.8569
92 6BK 0.8561
93 7EL 0.8561
94 CA4 0.8560
95 123 0.8552
96 2V4 0.8545
97 7G0 0.8539
98 RHN 0.8539
99 6WL 0.8538
100 1V1 0.8527
101 SZ5 0.8526
102 OAL 0.8518
103 7G2 0.8516
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 1VYP; Ligand: FMN; Similar sites found with APoc: 2
This union binding pocket(no: 1) in the query (biounit: 1vyp.bio1) has 27 residues
No: Leader PDB Ligand Sequence Similarity
1 3B0P FMN 4.28571
2 3B0P FMN 4.28571
Pocket No.: 2; Query (leader) PDB : 1VYP; Ligand: TNF; Similar sites found with APoc: 2
This union binding pocket(no: 2) in the query (biounit: 1vyp.bio1) has 26 residues
No: Leader PDB Ligand Sequence Similarity
1 3B0P FMN 4.28571
2 3B0P FMN 4.28571
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