scPDB - 4kfq entry

Protein Data Bank Entry:

PDB ID : 4kfq

Resolution :2.200 Å

Experimental Method : X-ray

Deposition Date : 2013-04-27

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Glutamate receptor ionotropic, NMDA 1
ID:	NMDZ1_RAT
AC:	P35439
Organism:	Rattus norvegicus
Reign:	Eukaryota
TaxID:	10116
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	17.916
Number of residues:	20
Including
Standard Amino Acids:	20
Non Standard Amino Acids:	0
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.098	1059.750

% Hydrophobic	% Polar
43.63	56.37
According to VolSite

Ligand :

HET Code:	KFQ
Formula:	C9H5N4OS
Molecular weight:	217.227 g/mol
DrugBank ID:	-
Buried Surface Area:	69.14 %
Polar Surface area:	79.71 Å2

Number of
H-Bond Acceptors:	4
H-Bond Donors:	1
Rings:	3
Aromatic rings:	2
Anionic atoms:	1
Cationic atoms:	0
Rule of Five Violation:	0
Rotatable Bonds:	0

Mass center Coordinates

X	Y	Z
8.76367	62.6275	7.90147

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
CAC	CG	GLN- 13	4.26	0	Hydrophobic	false
CAL	CZ	PHE- 92	3.3	0	Hydrophobic	false
CAE	CB	PRO- 124	4.17	0	Hydrophobic	false
NAI	O	PRO- 124	2.68	156.89	H-Bond (Ligand Donor)	false
OAA	N	THR- 126	2.84	178.85	H-Bond (Protein Donor)	false
OAA	NH1	ARG- 131	2.75	163.12	H-Bond (Protein Donor)	false
NAG	NH2	ARG- 131	3	159.08	H-Bond (Protein Donor)	false
NAH	OG	SER- 180	2.71	140.34	H-Bond (Ligand Donor)	false
CAC	CB	ASP- 224	3.87	0	Hydrophobic	false
CAC	CG2	VAL- 227	4.26	0	Hydrophobic	false