scPDB - 4qdk entry

Protein Data Bank Entry:

PDB ID : 4qdk

Resolution :1.700 Å

Experimental Method : X-ray

Deposition Date : 2014-05-14

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Magnesium-protoporphyrin O-methyltransferase
ID:	CHLM_SYNY3
AC:	Q55467
Organism:	Synechocystis sp.
Reign:	Bacteria
TaxID:	1111708
EC Number:	2.1.1.11

Chains:

Chain Name:	Percentage of Residues within binding site
A	100 %

Ligand binding site composition:

B-Factor:	15.242
Number of residues:	40
Including
Standard Amino Acids:	36
Non Standard Amino Acids:	0
Water Molecules:	4
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.638	243.000

% Hydrophobic	% Polar
61.11	38.89
According to VolSite

Ligand :

HET Code:	SAH
Formula:	C14H20N6O5S
Molecular weight:	384.411 g/mol
DrugBank ID:	DB01752
Buried Surface Area:	77.42 %
Polar Surface area:	212.38 Å2

Number of
H-Bond Acceptors:	10
H-Bond Donors:	4
Rings:	3
Aromatic rings:	2
Anionic atoms:	1
Cationic atoms:	1
Rule of Five Violation:	1
Rotatable Bonds:	7

Mass center Coordinates

X	Y	Z
20.7078	3.86823	10.7725

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
SD	CE2	PHE- 16	4.19	0	Hydrophobic	false
C5'	CZ	PHE- 16	4.1	0	Hydrophobic	false
C3'	CE2	PHE- 16	3.65	0	Hydrophobic	false
C2'	CD1	PHE- 16	3.53	0	Hydrophobic	false
SD	CE2	TYR- 28	3.97	0	Hydrophobic	false
CB	CE2	TYR- 28	4.28	0	Hydrophobic	false
O	NE2	HIS- 44	2.65	129.59	H-Bond (Protein Donor)	false
OXT	NE2	HIS- 44	2.81	155.5	H-Bond (Protein Donor)	false
N	O	GLY- 70	2.69	159.04	H-Bond (Ligand Donor)	false
O3'	OD1	ASP- 91	3.42	131.23	H-Bond (Ligand Donor)	false
O3'	OD2	ASP- 91	2.81	173.57	H-Bond (Ligand Donor)	false
O2'	OD1	ASP- 91	2.56	157.73	H-Bond (Ligand Donor)	false
N3	N	ILE- 92	3.19	147.27	H-Bond (Protein Donor)	false
C1'	CG2	ILE- 92	4.34	0	Hydrophobic	false
N6	OD1	ASP- 120	2.93	150.5	H-Bond (Ligand Donor)	false
N1	N	LEU- 121	2.94	173.62	H-Bond (Protein Donor)	false
N	O	LEU- 134	2.79	150.71	H-Bond (Ligand Donor)	false
CG	CB	ASP- 135	4.26	0	Hydrophobic	false
C5'	CG2	VAL- 136	4.06	0	Hydrophobic	false
N7	OH	TYR- 140	2.59	176.83	H-Bond (Protein Donor)	false
N6	OH	TYR- 140	3.05	160.89	H-Bond (Ligand Donor)	false
N	O	HOH- 402	2.91	151.25	H-Bond (Ligand Donor)	false
O	O	HOH- 412	2.78	160.65	H-Bond (Protein Donor)	false