scPDB - 4bv9 entry

Protein Data Bank Entry:

PDB ID : 4bv9

Resolution :2.190 Å

Experimental Method : X-ray

Deposition Date : 2013-06-25

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Ketimine reductase mu-crystallin
ID:	CRYM_MOUSE
AC:	O54983
Organism:	Mus musculus
Reign:	Eukaryota
TaxID:	10090
EC Number:	1.5.1.25

Chains:

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

Ligand binding site composition:

B-Factor:	23.504
Number of residues:	51
Including
Standard Amino Acids:	46
Non Standard Amino Acids:	0
Water Molecules:	5
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.325	1080.000

% Hydrophobic	% Polar
51.25	48.75
According to VolSite

Ligand :

HET Code:	NDP
Formula:	C21H26N7O17P3
Molecular weight:	741.389 g/mol
DrugBank ID:	DB02338
Buried Surface Area:	62.37 %
Polar Surface area:	404.9 Å2

Number of
H-Bond Acceptors:	22
H-Bond Donors:	5
Rings:	5
Aromatic rings:	2
Anionic atoms:	4
Cationic atoms:	0
Rule of Five Violation:	2
Rotatable Bonds:	13

Mass center Coordinates

X	Y	Z
23.265	15.5063	-7.26404

Binding mode :

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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
O1A	OG	SER- 90	2.62	169.46	H-Bond (Protein Donor)	false
O2D	NE2	HIS- 91	3.13	148.62	H-Bond (Ligand Donor)	false
C4N	CG2	THR- 115	3.63	0	Hydrophobic	false
O7N	NH1	ARG- 118	2.65	125.08	H-Bond (Protein Donor)	false
C4N	CG2	THR- 119	3.88	0	Hydrophobic	false
O3B	N	ALA- 143	2.92	162.78	H-Bond (Protein Donor)	false
O2A	N	VAL- 145	2.95	169.32	H-Bond (Protein Donor)	false
O2N	N	GLN- 146	3.02	173.61	H-Bond (Protein Donor)	false
C5D	CG	GLN- 146	4.22	0	Hydrophobic	false
O3B	OD1	ASN- 167	2.61	131.56	H-Bond (Ligand Donor)	false
O2B	ND2	ASN- 167	3.46	129.7	H-Bond (Protein Donor)	false
O2X	ND2	ASN- 167	2.52	153.59	H-Bond (Protein Donor)	false
O1X	NH2	ARG- 168	3.09	142.52	H-Bond (Protein Donor)	false
O1X	NE	ARG- 168	2.95	153.72	H-Bond (Protein Donor)	false
O3X	NH2	ARG- 168	3.46	144.03	H-Bond (Protein Donor)	false
O1X	CZ	ARG- 168	3.45	0	Ionic (Protein Cationic)	false
O1X	OG1	THR- 169	2.78	166.56	H-Bond (Protein Donor)	false
C5D	CB	VAL- 203	4.12	0	Hydrophobic	false
C1B	CB	THR- 204	4.35	0	Hydrophobic	false
O3D	O	THR- 204	3.15	164.1	H-Bond (Ligand Donor)	false
O4B	N	MET- 205	3.19	127.94	H-Bond (Protein Donor)	false
C3D	SD	MET- 205	3.5	0	Hydrophobic	false
C2D	CE	MET- 205	3.96	0	Hydrophobic	false
N7N	O	VAL- 225	3.42	155.68	H-Bond (Ligand Donor)	false
N7N	OG	SER- 291	3.24	151.42	H-Bond (Ligand Donor)	false
O1N	O	HOH- 2044	2.62	155.54	H-Bond (Protein Donor)	false
O2N	O	HOH- 2062	2.93	179.94	H-Bond (Protein Donor)	false