scPDB - 5cvc entry

Protein Data Bank Entry:

PDB ID : 5cvc

Resolution :2.090 Å

Experimental Method : X-ray

Deposition Date : 2015-07-26

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Serine racemase
ID:	F5CAQ9_MAIZE
AC:	F5CAQ9
Organism:	Zea mays
Reign:	Eukaryota
TaxID:	4577
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	24.313
Number of residues:	35
Including
Standard Amino Acids:	32
Non Standard Amino Acids:	0
Water Molecules:	3
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.953	982.125

% Hydrophobic	% Polar
39.86	60.14
According to VolSite

Ligand :

HET Code:	PLP
Formula:	C8H8NO6P
Molecular weight:	245.126 g/mol
DrugBank ID:	DB00114
Buried Surface Area:	72.92 %
Polar Surface area:	132.42 Å2

Number of
H-Bond Acceptors:	7
H-Bond Donors:	1
Rings:	1
Aromatic rings:	1
Anionic atoms:	2
Cationic atoms:	0
Rule of Five Violation:	0
Rotatable Bonds:	4

Mass center Coordinates

X	Y	Z
-16.6343	-31.0921	-4.48627

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
C4A	CZ	PHE- 66	4.15	0	Hydrophobic	false
C5A	CZ	PHE- 66	4.13	0	Hydrophobic	false
C4A	CD	LYS- 67	4.24	0	Hydrophobic	false
C4	CE	LYS- 67	4.07	0	Hydrophobic	false
O3	ND2	ASN- 94	2.82	159.86	H-Bond (Protein Donor)	false
C5A	CB	SER- 193	3.61	0	Hydrophobic	false
O1P	N	SER- 193	2.88	153.98	H-Bond (Protein Donor)	false
O3P	N	GLY- 194	2.81	158.65	H-Bond (Protein Donor)	false
O1P	N	GLY- 195	2.91	154.43	H-Bond (Protein Donor)	false
O2P	N	LEU- 197	2.89	158.5	H-Bond (Protein Donor)	false
C5	CD2	LEU- 247	3.81	0	Hydrophobic	false
C2A	CG	GLU- 290	4.09	0	Hydrophobic	false
C2A	CB	SER- 292	4.04	0	Hydrophobic	false
N1	OG	SER- 322	2.63	151.74	H-Bond (Protein Donor)	false
C2A	CB	SER- 322	3.95	0	Hydrophobic	false
O1P	O	HOH- 504	2.59	168.58	H-Bond (Protein Donor)	false
O2P	O	HOH- 508	2.61	164.45	H-Bond (Protein Donor)	false