scPDB - 3gdp entry

Protein Data Bank Entry:

PDB ID : 3gdp

Resolution :1.570 Å

Experimental Method : X-ray

Deposition Date : 2009-02-24

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	(R)-mandelonitrile lyase 2
ID:	MDL2_PRUDU
AC:	Q945K2
Organism:	Prunus dulcis
Reign:	Eukaryota
TaxID:	3755
EC Number:	4.1.2.10

Chains:

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

Ligand binding site composition:

B-Factor:	8.613
Number of residues:	72
Including
Standard Amino Acids:	63
Non Standard Amino Acids:	0
Water Molecules:	9
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.753	506.250

% Hydrophobic	% Polar
66.00	34.00
According to VolSite

Ligand :

HET Code:	FAD
Formula:	C27H31N9O15P2
Molecular weight:	783.534 g/mol
DrugBank ID:	DB03147
Buried Surface Area:	77.67 %
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
72.0458	-4.59074	-32.768

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
O1A	OG1	THR- 36	2.78	158.19	H-Bond (Protein Donor)	false
O1A	N	THR- 36	3.05	170.08	H-Bond (Protein Donor)	false
O4'	OG1	THR- 36	2.62	160.71	H-Bond (Ligand Donor)	false
C4'	CB	THR- 36	4.14	0	Hydrophobic	false
O1P	N	SER- 37	3.1	160.49	H-Bond (Protein Donor)	false
O3B	OE1	GLU- 55	2.77	170.62	H-Bond (Ligand Donor)	false
O2B	OE2	GLU- 55	2.7	164.01	H-Bond (Ligand Donor)	false
O2B	NE	ARG- 56	2.84	168.83	H-Bond (Protein Donor)	false
N3A	N	ARG- 56	3.17	145.27	H-Bond (Protein Donor)	false
C1B	CG	ARG- 56	4.15	0	Hydrophobic	false
C7M	CE1	PHE- 72	4.36	0	Hydrophobic	false
C7M	CD2	LEU- 76	4.16	0	Hydrophobic	false
C7M	CG2	VAL- 98	3.95	0	Hydrophobic	false
C8M	CG2	VAL- 98	3.69	0	Hydrophobic	false
O1A	N	THR- 106	2.91	156.28	H-Bond (Protein Donor)	false
O2A	OG1	THR- 106	2.87	171.9	H-Bond (Protein Donor)	false
C4'	CB	THR- 106	4.29	0	Hydrophobic	false
C8M	CG2	THR- 106	3.47	0	Hydrophobic	false
C9	CG2	THR- 106	3.48	0	Hydrophobic	false
C3'	CG2	THR- 106	4.25	0	Hydrophobic	false
C8M	CD1	ILE- 109	4.38	0	Hydrophobic	false
O2'	ND2	ASN- 110	3.24	174.09	H-Bond (Protein Donor)	false
C9A	CB	ASN- 110	3.54	0	Hydrophobic	false
N5	N	ALA- 111	3.11	173.56	H-Bond (Protein Donor)	false
N3	O	VAL- 113	2.78	156.34	H-Bond (Ligand Donor)	false
O4	N	VAL- 113	2.95	147.83	H-Bond (Protein Donor)	false
N6A	O	VAL- 217	2.94	166.5	H-Bond (Ligand Donor)	false
N1A	N	VAL- 217	3.07	155.56	H-Bond (Protein Donor)	false
C7M	CD2	TRP- 458	3.73	0	Hydrophobic	false
C6	CE3	TRP- 458	3.4	0	Hydrophobic	false
C8	CB	TRP- 458	3.39	0	Hydrophobic	false
O2P	N	GLY- 487	2.88	158.5	H-Bond (Protein Donor)	false
C1'	CG	PRO- 498	4.1	0	Hydrophobic	false
O2	N	GLN- 499	2.79	157.91	H-Bond (Protein Donor)	false
C2'	CB	GLN- 499	4.34	0	Hydrophobic	false
C4'	CD1	TYR- 502	3.83	0	Hydrophobic	false
O2	O	HOH- 694	2.85	179.96	H-Bond (Protein Donor)	false
O1P	O	HOH- 831	2.87	179.96	H-Bond (Protein Donor)	false
O2P	O	HOH- 835	2.78	148.31	H-Bond (Protein Donor)	false
N6A	O	HOH- 845	2.96	152.4	H-Bond (Ligand Donor)	false
N7A	O	HOH- 853	2.85	179.97	H-Bond (Protein Donor)	false
O3'	O	HOH- 879	2.85	164.04	H-Bond (Ligand Donor)	false