scPDB - 4lcw entry

Protein Data Bank Entry:

PDB ID : 4lcw

Resolution :2.400 Å

Experimental Method : X-ray

Deposition Date : 2013-06-24

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Major histocompatibility complex class I-related gene protein
ID:	HMR1_HUMAN
AC:	Q95460
Organism:	Homo sapiens
Reign:	Eukaryota
TaxID:	9606
EC Number:	/

Chains:

Chain Name:	Percentage of Residues within binding site
C	83 %
D	10 %
E	7 %

Ligand binding site composition:

B-Factor:	23.213
Number of residues:	32
Including
Standard Amino Acids:	30
Non Standard Amino Acids:	0
Water Molecules:	2
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.790	286.875

% Hydrophobic	% Polar
60.00	40.00
According to VolSite

Ligand :

HET Code:	1VY
Formula:	C12H16N4O7
Molecular weight:	328.278 g/mol
DrugBank ID:	-
Buried Surface Area:	73.96 %
Polar Surface area:	175.27 Å2

Number of
H-Bond Acceptors:	10
H-Bond Donors:	6
Rings:	2
Aromatic rings:	0
Anionic atoms:	0
Cationic atoms:	0
Rule of Five Violation:	2
Rotatable Bonds:	5

Mass center Coordinates

X	Y	Z
-133.475	38.2985	119.698

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
C9	CZ	TYR- 7	3.95	0	Hydrophobic	false
C1'	CD2	TYR- 7	3.63	0	Hydrophobic	false
O2	NH2	ARG- 9	3.15	125.44	H-Bond (Protein Donor)	false
O2	NE	ARG- 9	2.62	143.86	H-Bond (Protein Donor)	false
O4'	NH2	ARG- 9	2.79	136.79	H-Bond (Protein Donor)	false
N3	OG	SER- 24	2.82	159.96	H-Bond (Ligand Donor)	false
C9	CE1	TYR- 62	3.35	0	Hydrophobic	false
C4'	CZ2	TRP- 69	4.01	0	Hydrophobic	false
C3'	CH2	TRP- 69	3.82	0	Hydrophobic	false
O3'	NH1	ARG- 94	3.07	150.71	H-Bond (Protein Donor)	false
O2'	OH	TYR- 95	2.75	166.43	H-Bond (Protein Donor)	false
C5'	CD1	ILE- 96	3.52	0	Hydrophobic	false
O5'	OH	TYR- 152	2.75	130.85	H-Bond (Protein Donor)	false
O5'	OE1	GLN- 153	3.48	177.66	H-Bond (Ligand Donor)	false
C2'	CZ2	TRP- 156	3.47	0	Hydrophobic	false
O2	O	HOH- 407	2.88	166.6	H-Bond (Protein Donor)	false