scPDB - 3c7d entry

Protein Data Bank Entry:

PDB ID : 3c7d

Resolution :2.500 Å

Experimental Method : X-ray

Deposition Date : 2008-02-07

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Octopine dehydrogenase
ID:	OCDH_PECMA
AC:	Q9BHM6
Organism:	Pecten maximus
Reign:	Eukaryota
TaxID:	6579
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	30.265
Number of residues:	36
Including
Standard Amino Acids:	36
Non Standard Amino Acids:	0
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.015	1333.125

% Hydrophobic	% Polar
40.51	59.49
According to VolSite

Ligand :

HET Code:	NAD
Formula:	C21H26N7O14P2
Molecular weight:	662.417 g/mol
DrugBank ID:	-
Buried Surface Area:	50.84 %
Polar Surface area:	343.54 Å2

Number of
H-Bond Acceptors:	18
H-Bond Donors:	6
Rings:	5
Aromatic rings:	3
Anionic atoms:	2
Cationic atoms:	1
Rule of Five Violation:	3
Rotatable Bonds:	11

Mass center Coordinates

X	Y	Z
38.4024	14.757	-20.0545

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
O2A	N	ASN- 12	3.12	163.2	H-Bond (Protein Donor)	false
O1N	ND2	ASN- 12	2.73	152.46	H-Bond (Protein Donor)	false
O2N	N	GLY- 13	2.98	157.44	H-Bond (Protein Donor)	false
DuAr	DuAr	PHE- 35	3.98	0	Aromatic Face/Face	false
C2B	CD2	PHE- 35	3.66	0	Hydrophobic	false
O3B	OE2	GLU- 38	2.67	172.01	H-Bond (Ligand Donor)	false
O2B	OE1	GLU- 38	2.75	162.97	H-Bond (Ligand Donor)	false
C4B	CG1	VAL- 90	4.05	0	Hydrophobic	false
C1B	CG1	VAL- 90	3.88	0	Hydrophobic	false
C4D	CG	PRO- 116	4.32	0	Hydrophobic	false
C5N	CB	LEU- 144	3.86	0	Hydrophobic	false
C3N	CD2	LEU- 144	3.79	0	Hydrophobic	false
O7N	N	CYS- 148	2.78	161.78	H-Bond (Protein Donor)	false
N7N	O	CYS- 148	3.33	143.27	H-Bond (Ligand Donor)	false
O1A	NH2	ARG- 324	3.14	132.28	H-Bond (Protein Donor)	false