scPDB - 3zfd entry

Protein Data Bank Entry:

PDB ID : 3zfd

Resolution :1.710 Å

Experimental Method : X-ray

Deposition Date : 2012-12-11

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Chromosome-associated kinesin KIF4
ID:	KIF4_MOUSE
AC:	P33174
Organism:	Mus musculus
Reign:	Eukaryota
TaxID:	10090
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	9.415
Number of residues:	39
Including
Standard Amino Acids:	34
Non Standard Amino Acids:	1
Water Molecules:	4
Cofactors:
Metals:	MG

Cavity properties

Ligandability	Volume (Å3)
0.176	253.125

% Hydrophobic	% Polar
50.67	49.33
According to VolSite

Ligand :

HET Code:	ANP
Formula:	C10H13N6O12P3
Molecular weight:	502.164 g/mol
DrugBank ID:	-
Buried Surface Area:	60.48 %
Polar Surface area:	322.68 Å2

Number of
H-Bond Acceptors:	16
H-Bond Donors:	4
Rings:	3
Aromatic rings:	2
Anionic atoms:	4
Cationic atoms:	0
Rule of Five Violation:	2
Rotatable Bonds:	8

Mass center Coordinates

X	Y	Z
-20.5715	6.47884	24.5894

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
O2G	OG1	THR- 90	2.65	164.86	H-Bond (Protein Donor)	false
O1B	N	GLY- 93	2.89	155.56	H-Bond (Protein Donor)	false
O3A	N	GLY- 93	3.41	129.02	H-Bond (Protein Donor)	false
O1B	N	LYS- 94	2.86	158.94	H-Bond (Protein Donor)	false
O1B	NZ	LYS- 94	2.82	150.55	H-Bond (Protein Donor)	false
O3G	NZ	LYS- 94	2.82	163.39	H-Bond (Protein Donor)	false
O1B	NZ	LYS- 94	2.82	0	Ionic (Protein Cationic)	false
O3G	NZ	LYS- 94	2.82	0	Ionic (Protein Cationic)	false
O2B	N	THR- 95	3.02	160.12	H-Bond (Protein Donor)	false
O1A	N	TYR- 96	2.7	166.19	H-Bond (Protein Donor)	false
C2'	CD1	TYR- 96	4.14	0	Hydrophobic	false
DuAr	DuAr	TYR- 96	3.99	0	Aromatic Face/Face	false
O2A	ND2	ASN- 207	3	158.27	H-Bond (Protein Donor)	false
O2G	ND2	ASN- 207	3.38	139.31	H-Bond (Protein Donor)	false
O2G	OG	SER- 210	2.74	166.31	H-Bond (Protein Donor)	false
O1G	N	SER- 211	2.79	158.67	H-Bond (Protein Donor)	false
O1G	MG	MG- 500	1.97	0	Metal Acceptor	false
O2B	MG	MG- 500	2.04	0	Metal Acceptor	false
N6	O	HOH- 2016	2.88	164.68	H-Bond (Ligand Donor)	false
O3G	O	HOH- 2172	2.71	151.81	H-Bond (Protein Donor)	false