scPDB - 3pm9 entry

Protein Data Bank Entry:

PDB ID : 3pm9

Resolution :2.570 Å

Experimental Method : X-ray

Deposition Date : 2010-11-16

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Putative oxidoreductase
ID:	Q6NAV4_RHOPA
AC:	Q6NAV4
Organism:	Rhodopseudomonas palustris
Reign:	Bacteria
TaxID:	258594
EC Number:	/

Chains:

Chain Name:	Percentage of Residues within binding site
E	97 %
F	3 %

Ligand binding site composition:

B-Factor:	36.273
Number of residues:	70
Including
Standard Amino Acids:	65
Non Standard Amino Acids:	1
Water Molecules:	4
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.326	1225.125

% Hydrophobic	% Polar
50.96	49.04
According to VolSite

Ligand :

HET Code:	FAD
Formula:	C27H31N9O15P2
Molecular weight:	783.534 g/mol
DrugBank ID:	DB03147
Buried Surface Area:	76.49 %
Polar Surface area:	381.7 Å2

Number of
H-Bond Acceptors:	22
H-Bond Donors:	7
Rings:	6
Aromatic rings:	3
Anionic atoms:	2
Cationic atoms:	0
Rule of Five Violation:	3
Rotatable Bonds:	13

Mass center Coordinates

X	Y	Z
36.8784	179.86	-15.8039

Binding mode :

What is Poseview ?

2D View
3D View

Image generated by PoseView

Protein

Binding Site

Ligand

Interaction pattern

hydrophobic (CA)

aromatic (CZ)

hydrogen bond acceptor (O)

hydrogen bond acceptor/donor (OG)

hydrogen bond donor (N)

positively ionized (NZ)

negatively ionized (OD1)

metal (ZN)

Legend:

Represent the protein/ligand binding mode, centered on the ligand
Dashed lines represents hydrogen bonds and metal interactions
Green residue labels for amino acids with hydrophobic contacts (green lines) to the ligand

Image generated using PoseView by BioSolveIT

Ligand	Protein		Interaction
Atom	Atom	Residue	Distance (Å)	Angle (°)	Type
C8M	CB	GLU- 43	4.34	0	Hydrophobic	false
O2B	O	PRO- 79	2.58	151.05	H-Bond (Ligand Donor)	false
O1A	N	GLY- 81	2.68	156.48	H-Bond (Protein Donor)	false
O1P	N	GLY- 82	2.69	167.76	H-Bond (Protein Donor)	false
O1A	N	ASN- 83	2.91	145.4	H-Bond (Protein Donor)	false
C8M	CB	THR- 84	4.35	0	Hydrophobic	false
C9	CB	THR- 84	4.37	0	Hydrophobic	false
C3'	CB	THR- 84	4.06	0	Hydrophobic	false
O2P	N	THR- 84	2.94	157.69	H-Bond (Protein Donor)	false
O2P	OG1	THR- 84	2.56	165.56	H-Bond (Protein Donor)	false
O2A	N	GLY- 85	2.69	149.8	H-Bond (Protein Donor)	false
C8M	CD2	LEU- 86	4.14	0	Hydrophobic	false
C1'	CD1	LEU- 86	4.03	0	Hydrophobic	false
C9	CD1	LEU- 86	3.69	0	Hydrophobic	false
C5B	CB	GLN- 90	4.33	0	Hydrophobic	false
C3B	CB	GLN- 90	3.84	0	Hydrophobic	false
C8	CB	ALA- 145	3.84	0	Hydrophobic	false
C4'	CB	CYS- 149	4.03	0	Hydrophobic	false
O1P	OG1	THR- 150	2.87	171.55	H-Bond (Protein Donor)	false
O1P	N	THR- 150	2.91	158.26	H-Bond (Protein Donor)	false
O4'	OD1	ASN- 154	3.5	148.62	H-Bond (Ligand Donor)	false
C1B	CB	SER- 156	3.72	0	Hydrophobic	false
O4'	OG1	THR- 157	2.93	154.49	H-Bond (Protein Donor)	false
C5'	CG2	THR- 157	4.03	0	Hydrophobic	false
C5B	CG2	THR- 157	3.68	0	Hydrophobic	false
O2	N	GLY- 160	3.17	162.69	H-Bond (Protein Donor)	false
N3	O	GLY- 160	2.76	163.15	H-Bond (Ligand Donor)	false
O3B	O	GLU- 210	2.88	148.23	H-Bond (Ligand Donor)	false
N6A	O	ILE- 216	2.95	175.18	H-Bond (Ligand Donor)	false
N1A	N	ILE- 216	2.94	150.96	H-Bond (Protein Donor)	false
O2'	O	HOH- 601	2.66	179.99	H-Bond (Protein Donor)	false