Receptor
PDB id Resolution Class Description Source Keywords
2YNM 2.1 Å EC: 1.3.7.7 STRUCTURE OF THE ADPXALF3-STABILIZED TRANSITION STATE OF THE NITROGENASE-LIKE DARK-OPERATIVE PROTOCHLOROPHYLLIDE OXIDOREC OMPLEX FROM PROCHLOROCOCCUS MARINUS WITH ITS SUBSTRATE PR OTOCHLOROPHYLLIDE A PROCHLOROCOCCUS MARINUS IRON-SULFUR CLUSTER OXIDOREDUCTASE METALLOENZYME ELECTRONTRANSFER CHLOROPHYLL SYNTHESIS ATPASE DYNAMIC SWITCH
Ref.: STRUCTURE OF ADP-ALUMINIUM FLUORIDE-STABILIZED PROTOCHLOROPHYLLIDE OXIDOREDUCTASE COMPLEX. PROC.NATL.ACAD.SCI.USA V. 110 2094 2013
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
SF4 A:1302;
C:1413;
 Part of Protein;
Part of Protein;
 none;
none;
 submit data
351.64 Fe4 S4 [S]12...
EPE B:1296;
A:1297;
A:1298;
D:1529;
 Invalid;
Invalid;
Invalid;
Invalid;
 none;
none;
none;
none;
 submit data
238.305 C8 H18 N2 O4 S C1CN(...
MG A:1301;
B:1297;
 Part of Protein;
Part of Protein;
 none;
none;
 submit data
24.305 Mg [Mg+2...
ADP AF3 B:1298;
A:1299;
 Valid;
Valid;
 none;
none;
 submit data
n/a n/a
PMR C:1414;
 Valid;
 none;
 submit data
612.957 C35 H32 Mg N4 O5 CCC1=...
GOL D:1532;
A:1303;
D:1530;
C:1412;
 Invalid;
Invalid;
Invalid;
Invalid;
 none;
none;
none;
none;
 submit data
92.094 C3 H8 O3 C(C(C...
K D:1531;
 Part of Protein;
 none;
 submit data
39.098 K [K+]
1PE A:1296;
 Invalid;
 none;
 submit data
238.278 C10 H22 O6 C(COC...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
2YNM 2.1 Å EC: 1.3.7.7 STRUCTURE OF THE ADPXALF3-STABILIZED TRANSITION STATE OF THE NITROGENASE-LIKE DARK-OPERATIVE PROTOCHLOROPHYLLIDE OXIDOREC OMPLEX FROM PROCHLOROCOCCUS MARINUS WITH ITS SUBSTRATE PR OTOCHLOROPHYLLIDE A PROCHLOROCOCCUS MARINUS IRON-SULFUR CLUSTER OXIDOREDUCTASE METALLOENZYME ELECTRONTRANSFER CHLOROPHYLL SYNTHESIS ATPASE DYNAMIC SWITCH
Ref.: STRUCTURE OF ADP-ALUMINIUM FLUORIDE-STABILIZED PROTOCHLOROPHYLLIDE OXIDOREDUCTASE COMPLEX. PROC.NATL.ACAD.SCI.USA V. 110 2094 2013
Members (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1 families.
1 2YNM - ADP AF3 n/a n/a
70% Homology Family (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1 families.
1 2YNM - ADP AF3 n/a n/a
50% Homology Family (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1 families.
1 2YNM - ADP AF3 n/a n/a
Polypharmacology
Similar Ligands (2D)
Ligand no: 1; Ligand: ADP AF3; Similar ligands found: 0
No: Ligand ECFP6 Tc MDL keys Tc
Ligand no: 2; Ligand: PMR; Similar ligands found: 3
No: Ligand ECFP6 Tc MDL keys Tc
1 PMR 1 1
2 CLA 0.49697 0.866667
3 CHL 0.421348 0.866667
Similar Ligands (3D)
Ligand no: 1; Ligand: ADP AF3; Similar ligands found: 38
No: Ligand Similarity coefficient
1 ADP AF3 1.0000
2 ATP 0.9964
3 ADP 0.9881
4 ANP 0.9867
5 AGS 0.9674
6 ADP MG 0.9663
7 7DD 0.9519
8 ACP 0.9456
9 GCP 0.9434
10 GTP 0.9408
11 GNP 0.9407
12 GDP 0.9391
13 GSP 0.9389
14 7DT 0.9373
15 GDP BEF 0.9370
16 DAT 0.9270
17 ATP MG 0.9252
18 BEF ADP 0.9233
19 GDP ALF 0.9225
20 ALF GDP 0.9189
21 9GM 0.9185
22 DTP 0.9091
23 GDP AF3 0.9086
24 ADX 0.9055
25 ADP ALF 0.9048
26 ADP BEF 0.9031
27 ADP VO4 0.9009
28 GDP MG 0.8983
29 DBG 0.8970
30 BEF GDP 0.8967
31 AU1 0.8823
32 GNH 0.8807
33 G5A 0.8739
34 DGI 0.8706
35 M7G 0.8679
36 APC 0.8583
37 CTP 0.8574
38 UTP 0.8554
Ligand no: 2; Ligand: PMR; Similar ligands found: 0
No: Ligand Similarity coefficient
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 2YNM; Ligand: PMR; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 1) in the query (biounit: 2ynm.bio1) has 26 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 2; Query (leader) PDB : 2YNM; Ligand: PMR; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 2) in the query (biounit: 2ynm.bio1) has 26 residues
No: Leader PDB Ligand Sequence Similarity
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