scPDB - 4cdm entry

Protein Data Bank Entry:

PDB ID : 4cdm

Resolution :2.700 Å

Experimental Method : X-ray

Deposition Date : 2013-11-01

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Deoxyribodipyrimidine photolyase
ID:	Q8PYK9_METMA
AC:	Q8PYK9
Organism:	Methanosarcina mazei
Reign:	Archaea
TaxID:	192952
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	15.290
Number of residues:	41
Including
Standard Amino Acids:	36
Non Standard Amino Acids:	0
Water Molecules:	5
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.292	715.500

% Hydrophobic	% Polar
51.42	48.58
According to VolSite

Ligand :

HET Code:	FO1
Formula:	C16H17N3O7
Molecular weight:	363.322 g/mol
DrugBank ID:	-
Buried Surface Area:	61.35 %
Polar Surface area:	162.91 Å2

Number of
H-Bond Acceptors:	9
H-Bond Donors:	6
Rings:	3
Aromatic rings:	1
Anionic atoms:	0
Cationic atoms:	0
Rule of Five Violation:	1
Rotatable Bonds:	5

Mass center Coordinates

X	Y	Z
12.6042	30.0938	111.307

Binding mode :

What is Poseview ?

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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
N1	OG	SER- 26	3.4	129.93	H-Bond (Protein Donor)	false
O1	OG	SER- 26	2.88	171.33	H-Bond (Protein Donor)	false
C18	CB	SER- 26	4.43	0	Hydrophobic	false
O6	OG	SER- 26	2.65	169.58	H-Bond (Ligand Donor)	false
N2	O	CYS- 56	2.61	146.82	H-Bond (Ligand Donor)	false
O2	N	THR- 58	3.25	170.98	H-Bond (Protein Donor)	false
C7	CB	GLN- 68	4.29	0	Hydrophobic	false
C5	SD	MET- 72	3.62	0	Hydrophobic	false
O5	OG	SER- 118	2.99	159.56	H-Bond (Ligand Donor)	false
C18	CB	SER- 118	3.46	0	Hydrophobic	false
C18	CB	LYS- 123	3.62	0	Hydrophobic	false
O10	NE2	HIS- 272	2.64	164.17	H-Bond (Ligand Donor)	false
C9	CE1	PHE- 273	3.24	0	Hydrophobic	false
C7	CD	ARG- 411	3.97	0	Hydrophobic	false
O1	O	HOH- 2002	2.55	180	H-Bond (Protein Donor)	false
O3	O	HOH- 2003	2.67	156.89	H-Bond (Ligand Donor)	false
O6	O	HOH- 2016	2.56	179.01	H-Bond (Protein Donor)	false