scPDB - 4ccz entry

Protein Data Bank Entry:

PDB ID : 4ccz

Resolution :2.700 Å

Experimental Method : X-ray

Deposition Date : 2013-10-29

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Methionine synthase
ID:	METH_HUMAN
AC:	Q99707
Organism:	Homo sapiens
Reign:	Eukaryota
TaxID:	9606
EC Number:	2.1.1.13

Chains:

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

Ligand binding site composition:

B-Factor:	72.031
Number of residues:	32
Including
Standard Amino Acids:	32
Non Standard Amino Acids:	0
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.187	499.500

% Hydrophobic	% Polar
39.19	60.81
According to VolSite

Ligand :

HET Code:	THG
Formula:	C19H21N7O6
Molecular weight:	443.413 g/mol
DrugBank ID:	DB02031
Buried Surface Area:	54.16 %
Polar Surface area:	212.92 Å2

Number of
H-Bond Acceptors:	11
H-Bond Donors:	6
Rings:	3
Aromatic rings:	1
Anionic atoms:	2
Cationic atoms:	0
Rule of Five Violation:	2
Rotatable Bonds:	9

Mass center Coordinates

X	Y	Z
-26.8583	44.6505	0.712562

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
C6'	CG	GLU- 376	4.32	0	Hydrophobic	false
C5'	CB	GLU- 376	3.83	0	Hydrophobic	false
N	O	GLY- 382	2.97	164.01	H-Bond (Ligand Donor)	false
OE2	N	ARG- 384	3.11	126.36	H-Bond (Protein Donor)	false
N8	OD2	ASP- 449	3.1	172.96	H-Bond (Ligand Donor)	false
N1	ND2	ASN- 470	3.42	157.23	H-Bond (Protein Donor)	false
N2	OD1	ASN- 470	3.14	157.28	H-Bond (Ligand Donor)	false
N3	OD2	ASP- 537	2.84	132.31	H-Bond (Ligand Donor)	false
N2	OD2	ASP- 537	2.71	135.47	H-Bond (Ligand Donor)	false
C2'	CB	SER- 578	3.54	0	Hydrophobic	false
N5	OD1	ASN- 579	2.89	130.73	H-Bond (Ligand Donor)	false
OX2	CZ	ARG- 585	3.61	0	Ionic (Protein Cationic)	false
OX1	CZ	ARG- 585	3.59	0	Ionic (Protein Cationic)	false
OX2	CZ	ARG- 591	3.61	0	Ionic (Protein Cationic)	false
OX2	NH1	ARG- 591	2.7	168.84	H-Bond (Protein Donor)	false
O11	NH2	ARG- 591	2.86	136.89	H-Bond (Protein Donor)	false
C9	CG2	ILE- 611	4.11	0	Hydrophobic	false