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 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
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 Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 2YNM; Ligand: PMR; Similar sites found: 62
This union binding pocket(no: 1) in the query (biounit: 2ynm.bio1) has 26 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 1PEA ACM 0.003183 0.45679 2.65781
2 1Y42 TYR 0.004671 0.42369 3.06122
3 2Z9V PXM 0.00219 0.43771 3.31633
4 3P3N AKG 0.009778 0.42043 3.32226
5 4RPM HXC 0.04829 0.41769 3.94089
6 4DYO SD4 0.0117 0.40206 4.12371
7 1RZM PEP 0.007604 0.41465 4.14201
8 1V6A TRE 0.005762 0.42515 4.21687
9 3I8P 840 0.002174 0.41326 4.44965
10 1WDA BAG 0.003998 0.42136 4.46009
11 2F2U M77 0.0004762 0.45348 4.47761
12 1I0Z OXM 0.004574 0.45687 4.5045
13 1FW1 GSH 0.000532 0.44068 4.62963
14 2W47 UNF 0.01637 0.4098 4.86111
15 3MAG 3MA 0.01281 0.44164 4.88599
16 2Y7P SAL 0.001343 0.44676 5.04587
17 1Y9Q MED 0.00236 0.44863 5.20833
18 4RJK PYR 0.008669 0.43538 5.39906
19 3BY8 MLT 0.01285 0.4207 5.6338
20 1Q11 TYE 0.003589 0.42856 5.64516
21 3S9K CIT 0.005879 0.47113 5.9322
22 3MPI GRA 0.005612 0.40435 5.98007
23 2C5S AMP 0.004342 0.41989 6.64452
24 4F8L GAL 0.04126 0.4216 6.89655
25 2ZO9 MLI 0.005161 0.40981 6.93431
26 4C0X FMN 0.0002415 0.42083 7.38916
27 4LED XXR 0.001295 0.45738 7.46269
28 2QCX PF1 0.003279 0.43595 7.60456
29 4UYG 73B 0.02437 0.40968 7.64331
30 3QV9 QV7 0.001066 0.45744 8.01603
31 4COQ SAN 0.009656 0.42068 8.09717
32 2QLX RM4 0.0116 0.42282 8.33333
33 3QDT A2G GAL 0.03799 0.40357 8.39161
34 1G8S MET 0.01078 0.41849 8.69565
35 4LHM AZZ 0.01634 0.40513 9.15493
36 1QO0 BMD 0.02309 0.4033 9.18367
37 1ULE GLA GAL NAG 0.009295 0.43389 9.33333
38 3SHR CMP 0.002242 0.42657 9.36455
39 1O9U ADZ 0.003393 0.46352 10
40 1NNU TCT 0.002815 0.43004 10
41 3LTW HLZ 0.00112 0.46339 10.3571
42 1EYE PMM 0.001334 0.43045 10.3571
43 2Q37 3AL 0.001219 0.45488 10.4972
44 3DGB MUC 0.00516 0.40762 10.5634
45 3ZPG 5GP 0.01549 0.42967 11.2957
46 1TUV VK3 0.01235 0.43474 11.4035
47 1SQ5 ADP 0.004806 0.40882 11.6883
48 1SQ5 PAU 0.01335 0.40419 11.6883
49 3UEC ALA ARG TPO LYS 0.0188 0.41283 13.0137
50 2PP3 LGT 0.000806 0.43388 13.0653
51 4F4S EFO 0.002406 0.43597 13.1579
52 4IXW IXW 0.008769 0.40726 13.3858
53 2IYG FMN 0.002613 0.41911 14.5161
54 1YRX FMN 0.004699 0.40497 14.876
55 1T0S BML 0.0007093 0.48882 16.2791
56 1N9L FMN 0.002308 0.4043 16.5138
57 3KMT SAH 0.001407 0.42475 17.6471
58 3F81 STT 0.004406 0.45771 18.5792
59 2E1A MSE 0.005483 0.4157 18.6667
60 3PLN U5P 0.01556 0.40134 21.2625
61 1V7R CIT 0.009215 0.44932 23.1183
62 3RF4 FUN 0.001222 0.44851 23.2759
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