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Receptor
PDB id Resolution Class Description Source Keywords
3IQE 1.8 Å EC: 1.5.99.9 STRUCTURE OF F420 DEPENDENT METHYLENE-TETRAHYDROMETHANOPTERI DEHYDROGENASE IN COMPLEX WITH METHYLENE-TETRAHYDROMETHANOPTC OENZYME F420 METHANOPYRUS KANDLERI TERNARY COMPLEX OF PROTEIN SUBSTRATE AND CO-SUBSTRATE METHANOGENESIS ONE-CARBON METABOLISM OXIDOREDUCTASE
Ref.: STRUCTURAL BASIS OF THE HYDRIDE TRANSFER MECHANISM F(420)-DEPENDENT METHYLENETETRAHYDROMETHANOPTERIN DEHYDROGENASE BIOCHEMISTRY V. 48 10098 2009
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
CA B:286;
B:287;
C:286;
D:286;
Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
none;
none;
none;
none;
submit data
40.078 Ca [Ca+2...
F42 A:285;
B:285;
C:285;
D:285;
E:285;
F:285;
Valid;
Valid;
Valid;
Valid;
Valid;
Valid;
none;
none;
none;
none;
none;
none;
submit data
773.593 C29 H36 N5 O18 P C[C@@...
H4M A:284;
B:284;
C:284;
D:284;
E:284;
F:284;
Valid;
Valid;
Valid;
Valid;
Valid;
Valid;
none;
none;
none;
none;
none;
none;
submit data
788.693 C31 H45 N6 O16 P C[C@H...
NA C:287;
D:287;
E:286;
Part of Protein;
Part of Protein;
Part of Protein;
none;
none;
none;
submit data
22.99 Na [Na+]
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
3IQE 1.8 Å EC: 1.5.99.9 STRUCTURE OF F420 DEPENDENT METHYLENE-TETRAHYDROMETHANOPTERI DEHYDROGENASE IN COMPLEX WITH METHYLENE-TETRAHYDROMETHANOPTC OENZYME F420 METHANOPYRUS KANDLERI TERNARY COMPLEX OF PROTEIN SUBSTRATE AND CO-SUBSTRATE METHANOGENESIS ONE-CARBON METABOLISM OXIDOREDUCTASE
Ref.: STRUCTURAL BASIS OF THE HYDRIDE TRANSFER MECHANISM F(420)-DEPENDENT METHYLENETETRAHYDROMETHANOPTERIN DEHYDROGENASE BIOCHEMISTRY V. 48 10098 2009
Members (3)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1 families.
1 3IQZ - H4M C31 H45 N6 O16 P C[C@H]1[C@....
2 3IQE - F42 C29 H36 N5 O18 P C[C@@H](C(....
3 3IQF - E4M C31 H44 N6 O16 P C[C@H]1[C@....
70% Homology Family (3)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1 families.
1 3IQZ - H4M C31 H45 N6 O16 P C[C@H]1[C@....
2 3IQE - F42 C29 H36 N5 O18 P C[C@@H](C(....
3 3IQF - E4M C31 H44 N6 O16 P C[C@H]1[C@....
50% Homology Family (3)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1 families.
1 3IQZ - H4M C31 H45 N6 O16 P C[C@H]1[C@....
2 3IQE - F42 C29 H36 N5 O18 P C[C@@H](C(....
3 3IQF - E4M C31 H44 N6 O16 P C[C@H]1[C@....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: F42; Similar ligands found: 4
No: Ligand ECFP6 Tc MDL keys Tc
1 6J4 1 1
2 F42 1 1
3 FO1 0.508333 0.833333
4 HDF 0.508333 0.833333
Ligand no: 2; Ligand: H4M; Similar ligands found: 5
No: Ligand ECFP6 Tc MDL keys Tc
1 H4M 1 1
2 E4M 0.653595 0.94382
3 H4Z 0.645161 0.931818
4 N4M 0.559006 0.897727
5 F4M 0.554878 0.931818
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 3IQE; Ligand: F42; Similar sites found with APoc: 102
This union binding pocket(no: 1) in the query (biounit: 3iqe.bio1) has 31 residues
No: Leader PDB Ligand Sequence Similarity
1 1UO5 PIH None
2 1NU4 MLA None
3 3V2Q PLM None
4 1UO4 PIH None
5 6FX2 FUC C4W NAG BMA MAN NAG GAL None
6 3K56 IS3 1.8797
7 3X01 AMP 2.29008
8 1IYB 5GP 2.40385
9 3AQT RCO 2.44898
10 2CIX CEJ 2.4735
11 2CDU ADP 2.4735
12 5IKI A9H 2.4735
13 2VOH CIT 2.54777
14 5DCH 1YO 2.60417
15 4DE3 DN8 2.6616
16 3DTU DXC 2.67176
17 5UV1 0FV 2.82686
18 4RDL FUC GAL NDG FUC 2.82686
19 4B47 GDP 2.82686
20 3U6B GDP 2.82686
21 4JOB TLA 2.82686
22 4WGF HX2 2.92683
23 3VPQ GSH 2.94118
24 3Q85 GNP 2.95858
25 4YGF AZM 2.99145
26 4DKX GDP 3.24074
27 2ZO9 MLI 3.28467
28 3MAN BMA BMA MAN 3.31126
29 1XZ3 ICF 3.44828
30 4F06 PHB 3.53357
31 2BP1 FLC 3.53357
32 1GVE CIT 3.53357
33 1MT1 AG2 3.53982
34 1GUI BGC BGC BGC BGC BGC BGC 3.87097
35 4OEV OXL 3.88693
36 3BMO AX4 3.88693
37 4CM9 YGL 3.88693
38 2IDV M7G 3.9548
39 1HFE CYS 4.06504
40 6BYF CIT 4.11765
41 5JBX MLI 4.21456
42 3O01 DXC 4.24028
43 5LX9 OLB 4.24028
44 3ANY 2A3 4.24028
45 3TTN SPD 4.24028
46 5YT0 GDP 4.24028
47 5NM7 GLY 4.51128
48 5O74 GDP 4.56853
49 2OWZ CIT 4.59364
50 6F90 MVL 4.59364
51 3KP6 SAL 4.63576
52 5IUY BOG 5.30035
53 3GUZ PAF 5.68182
54 6GR0 F8W 5.74713
55 6DW2 HD4 5.88235
56 3MB3 MB3 5.92593
57 2I4O ATP 6.00707
58 5W3Y IHP 6.00707
59 2HZL PYR 6.36042
60 1PZL MYR 6.71378
61 6BND OPE 7.06714
62 1NJJ GET 7.06714
63 2ON5 GSH 7.28155
64 6DWI HD4 7.29614
65 4J0Q GDP 7.3903
66 4MRP GSH 7.42049
67 4UP4 NDG 7.42049
68 4UP4 NAG 7.42049
69 5X80 SAL 7.5
70 4L9I 8PR 7.77385
71 2P9H IPT 7.80669
72 4CVN ADP 8.0292
73 1VG1 GDP 8.10811
74 5OVV ACE ILE GLU SER THR GLU ILE 8.13008
75 1Q8A HCS 8.83392
76 3RV5 DXC 8.98876
77 3KYQ DPV 9.04523
78 4YDU ADP 9.2827
79 4V1F BQ1 9.30233
80 3FS1 MYR 9.54064
81 5OSW DIU 9.54064
82 5TCI MLI 9.54064
83 5C1M OLC 9.6
84 5EXK 5AD 9.89399
85 1T0S BML 10.4651
86 2D5X L35 10.6383
87 1MID LAP 10.989
88 1N13 AG2 13.2743
89 2QQC AG2 13.3929
90 2QQD AG2 13.3929
91 2V57 PRL 13.6842
92 4URX FK1 14.0541
93 1KZL CRM 14.4231
94 1GPJ CIT 15.1943
95 6BVK EAV 15.5689
96 6BVM EBV 15.5689
97 6BVL EBY 15.5689
98 6BVI EC4 15.5689
99 6BVJ EAS 15.5689
100 2HPL ASP ASP LEU TYR GLY 16
101 4AP9 1PS 17.9104
102 3CM2 X23 19.2308
Pocket No.: 2; Query (leader) PDB : 3IQE; Ligand: F42; Similar sites found with APoc: 35
This union binding pocket(no: 2) in the query (biounit: 3iqe.bio1) has 32 residues
No: Leader PDB Ligand Sequence Similarity
1 4Z7X 3CX 2.10084
2 1Q7E MET 2.12014
3 1J78 OLA 2.4735
4 5FUS DAO 2.4735
5 1H5R G1P 2.4735
6 1Z0A GDP 3.44828
7 2GN2 C5P 3.53357
8 5XNA SHV 3.62319
9 2OHV NHL 3.78788
10 4FXQ G9L 3.88693
11 6CB2 OLC 3.88693
12 5JDI 6JO 3.88693
13 4DVE BTN 4.0404
14 1Q5H DUD 4.08163
15 5MB4 NDG 4.24028
16 4OUE IPT 4.24028
17 5C9P FUC 4.24028
18 3U3U EAH 4.72103
19 3W68 4PT 5.26316
20 2J5V PCA 5.30035
21 6A46 DCM 5.46875
22 3E3U NVC 5.58376
23 4GLW NMN 6.00707
24 6C92 EGV 6.36042
25 3MG9 GHP 3MY 3FG GHP GHP OMY 3FG 6.71378
26 3RMK BML 7.06714
27 3HYW DCQ 7.77385
28 1EJH M7G 7.89474
29 3O5N BR0 8.92857
30 5W75 GDP 9.54064
31 5XL4 SIA 10.7955
32 3WMX THR 12.2905
33 5X2N ALA 13.7809
34 6H45 QEI 18.7279
35 5MWE TCE 42.8571
Pocket No.: 3; Query (leader) PDB : 3IQE; Ligand: F42; Similar sites found with APoc: 31
This union binding pocket(no: 3) in the query (biounit: 3iqe.bio1) has 30 residues
No: Leader PDB Ligand Sequence Similarity
1 1PZM 5GP 0.947867
2 6BMN PAP 1.76678
3 6I6X TLA 2.12014
4 1VRP IOM 2.12014
5 2YLN CYS 2.4735
6 5M04 GDP 2.4735
7 4UX9 ANP 2.4735
8 3U6K GDP 2.82686
9 2POC UD1 2.82686
10 1D8T GDP 2.82686
11 1ONI BEZ 2.89855
12 3GJB AKG 3.18021
13 5W7Q GDP 3.18021
14 5AVF TAU 3.50195
15 3BJC WAN 3.53357
16 3N5C GDP 4.32099
17 1ZX5 LFR 4.33333
18 5A1S FLC 4.59364
19 4XJ2 FMN 4.59364
20 3DAK ANP 5.65371
21 5UE4 5XQ 6.35593
22 3EC1 GDP 7.06714
23 2QN6 GDP 7.06714
24 4GV8 DUP 7.10059
25 1RE0 GDP 7.31707
26 1YRB GDP 7.63359
27 1VG9 GDP 8.10811
28 3G5N PB2 8.12721
29 5XSS XYP 8.12721
30 4P3Y GDP 8.24176
31 2HT6 GDP 9.1954
Pocket No.: 4; Query (leader) PDB : 3IQE; Ligand: H4M; Similar sites found with APoc: 66
This union binding pocket(no: 4) in the query (biounit: 3iqe.bio1) has 23 residues
No: Leader PDB Ligand Sequence Similarity
1 1UO5 PIH None
2 1UO4 PIH None
3 1NU4 MLA None
4 6FX2 FUC C4W NAG BMA MAN NAG GAL None
5 1UCD U5P None
6 2NLQ GLY None
7 3BP1 GUN 0.706714
8 2C91 TLA 1.76678
9 6I6X TLA 2.12014
10 6F5W KG1 2.12014
11 3K4Z XGP 2.12014
12 1Q7E MET 2.12014
13 3X01 AMP 2.29008
14 3AQT RCO 2.44898
15 2CIX CEJ 2.4735
16 1J78 OLA 2.4735
17 5FUS DAO 2.4735
18 4DE3 DN8 2.6616
19 3DTU DXC 2.67176
20 4RDL FUC GAL NDG FUC 2.82686
21 1ONI BEZ 2.89855
22 4WGF HX2 2.92683
23 1XZ3 ICF 3.44828
24 2BP1 FLC 3.53357
25 4F06 PHB 3.53357
26 1MT1 AG2 3.53982
27 5XNA SHV 3.62319
28 6CB2 OLC 3.88693
29 4DVE BTN 4.0404
30 1HFE CYS 4.06504
31 3O01 DXC 4.24028
32 5LX9 OLB 4.24028
33 5NM7 GLY 4.51128
34 2OWZ CIT 4.59364
35 3KP6 SAL 4.63576
36 5IUY BOG 5.30035
37 3GUZ PAF 5.68182
38 6GR0 F8W 5.74713
39 2I4O ATP 6.00707
40 2ZUX RAM 6.36042
41 1PZL MYR 6.71378
42 1NJJ GET 7.06714
43 4MRP GSH 7.42049
44 5X80 SAL 7.5
45 4OGQ 7PH 7.5
46 2AF6 BRU 7.75194
47 5OVV ACE ILE GLU SER THR GLU ILE 8.13008
48 3RV5 DXC 8.98876
49 3FS1 MYR 9.54064
50 5OSW DIU 9.54064
51 5TCI MLI 9.54064
52 5C1M OLC 9.6
53 1T0S BML 10.4651
54 2D5X L35 10.6383
55 1MID LAP 10.989
56 1N13 AG2 13.2743
57 2QQD AG2 13.3929
58 2QQC AG2 13.3929
59 2V57 PRL 13.6842
60 4URX FK1 14.0541
61 1KZL CRM 14.4231
62 6BVK EAV 15.5689
63 6BVM EBV 15.5689
64 6BVL EBY 15.5689
65 6BVI EC4 15.5689
66 6BVJ EAS 15.5689
Pocket No.: 5; Query (leader) PDB : 3IQE; Ligand: F42; Similar sites found with APoc: 8
This union binding pocket(no: 5) in the query (biounit: 3iqe.bio1) has 31 residues
No: Leader PDB Ligand Sequence Similarity
1 3VSV XYP 1.41343
2 4G0P U5P 2.04082
3 4TQK NAG 2.12014
4 4G86 BNT 2.4735
5 2ZL4 ALA ALA ALA ALA 3.57143
6 3QM1 ZYC 3.77358
7 4Y8D 49J 4.947
8 3KO0 TFP 10.8911
Pocket No.: 6; Query (leader) PDB : 3IQE; Ligand: H4M; Similar sites found with APoc: 10
This union binding pocket(no: 6) in the query (biounit: 3iqe.bio1) has 23 residues
No: Leader PDB Ligand Sequence Similarity
1 4G0P U5P 2.04082
2 5Z20 OXM 2.12014
3 4MGA 27L 2.7451
4 2GN2 C5P 3.53357
5 3GDN MXN 3.88693
6 4XJ2 FMN 4.59364
7 4TO8 FLC 8.83392
8 3O5N BR0 8.92857
9 4V1F BQ1 9.30233
10 4O4Z N2O 10.3896
Pocket No.: 7; Query (leader) PDB : 3IQE; Ligand: H4M; Similar sites found with APoc: 6
This union binding pocket(no: 7) in the query (biounit: 3iqe.bio1) has 23 residues
No: Leader PDB Ligand Sequence Similarity
1 4RW3 TDA 3.18021
2 5VLQ ANP 5.30035
3 2HZL PYR 6.36042
4 5V4R MGT 8.02469
5 3G5N PB2 8.12721
6 5X2N ALA 13.7809
Pocket No.: 8; Query (leader) PDB : 3IQE; Ligand: H4M; Similar sites found with APoc: 8
This union binding pocket(no: 8) in the query (biounit: 3iqe.bio1) has 24 residues
No: Leader PDB Ligand Sequence Similarity
1 2HYV UAP SGN IDS SGN IDS 1.76678
2 2XOC ADE 2.29885
3 3DUV KDO 2.67176
4 2IDV M7G 3.9548
5 6BYF CIT 4.11765
6 1RZM E4P 5.30035
7 1LVW TYD 5.65371
8 1GPJ CIT 15.1943
Pocket No.: 9; Query (leader) PDB : 3IQE; Ligand: H4M; Similar sites found with APoc: 2
This union binding pocket(no: 9) in the query (biounit: 3iqe.bio1) has 23 residues
No: Leader PDB Ligand Sequence Similarity
1 2ZL4 ALA ALA ALA ALA 3.57143
2 3KO0 TFP 10.8911
Pocket No.: 10; Query (leader) PDB : 3IQE; Ligand: F42; Similar sites found with APoc: 6
This union binding pocket(no: 10) in the query (biounit: 3iqe.bio1) has 30 residues
No: Leader PDB Ligand Sequence Similarity
1 2C91 TLA 1.76678
2 2CJW GDP 3.125
3 5VLQ ANP 5.30035
4 5GQX GLC GLC GLC GLC 9.18728
5 3BOF HCS 9.18728
6 4O4Z N2O 10.3896
Pocket No.: 11; Query (leader) PDB : 3IQE; Ligand: F42; Similar sites found with APoc: 9
This union binding pocket(no: 11) in the query (biounit: 3iqe.bio1) has 31 residues
No: Leader PDB Ligand Sequence Similarity
1 4TVD BGC 2.12014
2 2QLU ADE 3.88693
3 4COQ SAN 4.45344
4 4XBA 5GP 5
5 4B3J COA 5.65371
6 3HZT J60 6.00707
7 2AWN ADP 7.06714
8 4LCN GNG 7.61421
9 5V4R MGT 8.02469
Pocket No.: 12; Query (leader) PDB : 3IQE; Ligand: H4M; Similar sites found with APoc: 3
This union binding pocket(no: 12) in the query (biounit: 3iqe.bio1) has 23 residues
No: Leader PDB Ligand Sequence Similarity
1 1USR SIA WIA 5.30035
2 3MG9 GHP 3MY 3FG GHP GHP OMY 3FG 6.71378
3 1EJH M7G 7.89474
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