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Receptor
PDB id Resolution Class Description Source Keywords
2D0V 2.49 Å EC: 1.1.99.8 CRYSTAL STRUCTURE OF METHANOL DEHYDROGENASE FROM HYPHOMICROBIUM DENITRIFICANS HYPHOMICROBIUM DENITRIFICANS ELECTRON TRANSFER OXIDOREDUCTASE CALCIUM BINDING METHANOL PQQ
Ref.: CRYSTAL STRUCTURES OF CYTOCHROME C(L) AND METHANOL DEHYDROGENASE FROM HYPHOMICROBIUM DENITRIFICANS: STRUCTURAL AND MECHANISTIC INSIGHTS INTO INTERACTIONS BETWEEN THE TWO PROTEINS BIOCHEMISTRY V. 45 3481 2006
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
CA A:775;
D:775;
I:775;
Part of Protein;
Part of Protein;
Part of Protein;
none;
none;
none;
submit data
40.078 Ca [Ca+2...
PQQ A:601;
D:601;
I:601;
Valid;
Valid;
Valid;
none;
none;
none;
submit data
330.206 C14 H6 N2 O8 c1c2c...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
2D0V 2.49 Å EC: 1.1.99.8 CRYSTAL STRUCTURE OF METHANOL DEHYDROGENASE FROM HYPHOMICROBIUM DENITRIFICANS HYPHOMICROBIUM DENITRIFICANS ELECTRON TRANSFER OXIDOREDUCTASE CALCIUM BINDING METHANOL PQQ
Ref.: CRYSTAL STRUCTURES OF CYTOCHROME C(L) AND METHANOL DEHYDROGENASE FROM HYPHOMICROBIUM DENITRIFICANS: STRUCTURAL AND MECHANISTIC INSIGHTS INTO INTERACTIONS BETWEEN THE TWO PROTEINS BIOCHEMISTRY V. 45 3481 2006
Members (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 4 families.
1 2D0V - PQQ C14 H6 N2 O8 c1c2c([nH]....
70% Homology Family (5)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 2 families.
1 1G72 - PQQ C14 H6 N2 O8 c1c2c([nH]....
2 4AAH - PQQ C14 H6 N2 O8 c1c2c([nH]....
3 1W6S - PQQ C14 H6 N2 O8 c1c2c([nH]....
4 1H4I - PQQ C14 H6 N2 O8 c1c2c([nH]....
5 2D0V - PQQ C14 H6 N2 O8 c1c2c([nH]....
50% Homology Family (7)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1 families.
1 1G72 - PQQ C14 H6 N2 O8 c1c2c([nH]....
2 4AAH - PQQ C14 H6 N2 O8 c1c2c([nH]....
3 5XM3 - PQQ C14 H6 N2 O8 c1c2c([nH]....
4 1W6S - PQQ C14 H6 N2 O8 c1c2c([nH]....
5 1H4I - PQQ C14 H6 N2 O8 c1c2c([nH]....
6 2D0V - PQQ C14 H6 N2 O8 c1c2c([nH]....
7 1LRW - PQQ C14 H6 N2 O8 c1c2c([nH]....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: PQQ; Similar ligands found: 1
No: Ligand ECFP6 Tc MDL keys Tc
1 PQQ 1 1
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 2D0V; Ligand: PQQ; Similar sites found with APoc: 41
This union binding pocket(no: 1) in the query (biounit: 2d0v.bio2) has 23 residues
No: Leader PDB Ligand Sequence Similarity
1 2J5V PCA 1.90736
2 2WR9 MAN MAN 3.90625
3 4UP5 94W 4.0404
4 4W9N TCL 4.12979
5 1OIK AKG 4.16667
6 3A23 GAL 4.16667
7 1XX6 ADP 4.18848
8 1OIJ AKG 4.98339
9 1P0Z FLC 5.34351
10 5SWI BMA 5.55556
11 6FWH 5LD 5.55556
12 3G6M CFF 5.55556
13 6F8N NAG NAG 5.55556
14 5N17 8FK 5.7971
15 4KJG 4NP 6.94444
16 5X7Q GLC 6.94444
17 4L9Z OXL 7.07965
18 3C8F MT2 8.33333
19 6FXR AKG 8.33333
20 1GQ2 OXL 8.33333
21 2Z77 NCA 8.33333
22 1RZM PEP 8.33333
23 1O68 KIV 9.09091
24 5H4R CTT 9.72222
25 3RF4 FUN 9.72222
26 5D4Y BXP 11.1111
27 3EW2 BTN 12.5
28 6HLY G9Z 12.5
29 3CYQ AMU 13.0435
30 6G33 5ID 13.8889
31 6F6D AKG 15.2778
32 1B4U DHB 15.2778
33 4K6B GLU 15.2778
34 5D3X 4IP 15.5689
35 1IUP ALQ 16.6667
36 2ZUX RAM 18.0556
37 3CQ5 PMP 19.4444
38 4D4U FUC 19.4444
39 6HDT BTN 21.0526
40 4CVC PQQ 41.958
41 1YIQ PQQ 48.5762
Pocket No.: 2; Query (leader) PDB : 2D0V; Ligand: PQQ; Similar sites found with APoc: 23
This union binding pocket(no: 2) in the query (biounit: 2d0v.bio2) has 22 residues
No: Leader PDB Ligand Sequence Similarity
1 5W1E PHB 3.80228
2 2VN9 GVD 4.16667
3 6GG9 FMN 6.17284
4 2P9T 3PG 6.49038
5 3BRE C2E 6.94444
6 1R37 ETX 8.33333
7 2JFV FLC 8.33333
8 4BHL ARG 8.33333
9 5DEQ ARA 8.33333
10 5KJZ PCG 9.33333
11 1WPQ 13P 9.72222
12 4MJ0 SIA SIA 10.9091
13 1Z6K OAA 11.1111
14 3RGA LSB 13.8889
15 5VZ0 ADP 13.8889
16 4Z28 BTN 15.2778
17 1H4H XYP XYS XYP 15.2778
18 5AEW BNL 15.2778
19 6ACS CIT 18.0556
20 4K91 SIN 18.0556
21 1M3U KPL 19.4444
22 1Z5U CMP 19.4444
23 4RF7 ARG 22.2222
Pocket No.: 3; Query (leader) PDB : 2D0V; Ligand: PQQ; Similar sites found with APoc: 22
This union binding pocket(no: 3) in the query (biounit: 2d0v.bio1) has 22 residues
No: Leader PDB Ligand Sequence Similarity
1 1SGJ OAA 3.87324
2 4OUC 5ID 4.16667
3 2Y88 2ER 4.91803
4 5XXH E0D 5.55556
5 3BC9 ACR 5.55556
6 5I35 ANP 6.10687
7 2A9G ARG 8.33333
8 4BA5 PXG 8.33333
9 4ZUL UN1 9.72222
10 1HQS CIT 9.72222
11 2G3F IZC 9.72222
12 4C1K PEP 11.1111
13 1Z45 GAL 12.5
14 6AMI TRP 13.8889
15 5UFF 8B7 14.8148
16 3QUZ QUV 16.5975
17 4R9F BMA BMA 16.6667
18 2AY3 MPP 16.6667
19 1H5R THM 16.6667
20 5LXT GTP 18.0556
21 3ANY 2A3 18.0556
22 4OEV OXL 25
Pocket No.: 4; Query (leader) PDB : 2D0V; Ligand: PQQ; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 4) in the query (biounit: 2d0v.bio1) has 22 residues
No: Leader PDB Ligand Sequence Similarity
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