scPDB - 4neu entry

Protein Data Bank Entry:

PDB ID : 4neu

Resolution :2.570 Å

Experimental Method : X-ray

Deposition Date : 2013-10-30

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Receptor-interacting serine/threonine-protein kinase 1
ID:	RIPK1_HUMAN
AC:	Q13546
Organism:	Homo sapiens
Reign:	Eukaryota
TaxID:	9606
EC Number:	2.7.11.1

Chains:

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

Ligand binding site composition:

B-Factor:	56.526
Number of residues:	35
Including
Standard Amino Acids:	33
Non Standard Amino Acids:	0
Water Molecules:	2
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.402	597.375

% Hydrophobic	% Polar
56.50	43.50
According to VolSite

Ligand :

HET Code:	Q1A
Formula:	C23H23N5O2
Molecular weight:	401.461 g/mol
DrugBank ID:	-
Buried Surface Area:	63.42 %
Polar Surface area:	106.07 Å2

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

Mass center Coordinates

X	Y	Z
62.5182	66.1143	23.4063

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
C17	CD1	LEU- 23	4.36	0	Hydrophobic	false
C11	CG1	VAL- 31	4.42	0	Hydrophobic	false
C16	CG1	VAL- 31	3.83	0	Hydrophobic	false
C15	CG2	ILE- 43	4.11	0	Hydrophobic	false
C18	CD1	ILE- 43	4.17	0	Hydrophobic	false
C19	CG1	ILE- 43	3.69	0	Hydrophobic	false
C10	CD	LYS- 45	4.16	0	Hydrophobic	false
N01	OE2	GLU- 63	3.02	141.44	H-Bond (Ligand Donor)	false
N02	OE2	GLU- 63	2.93	142.2	H-Bond (Ligand Donor)	false
C01	CG	MET- 66	4.48	0	Hydrophobic	false
C04	CG	MET- 66	4.38	0	Hydrophobic	false
C01	CD1	LEU- 70	3.67	0	Hydrophobic	false
C04	CD1	LEU- 70	4.13	0	Hydrophobic	false
C01	CG1	VAL- 75	3.69	0	Hydrophobic	false
C03	CG1	VAL- 75	4.42	0	Hydrophobic	false
C22	CG2	VAL- 76	4.48	0	Hydrophobic	false
C14	CG2	VAL- 76	3.97	0	Hydrophobic	false
C10	SD	MET- 92	3.65	0	Hydrophobic	false
C14	SD	MET- 92	3.97	0	Hydrophobic	false
N03	O	MET- 95	3.09	138.57	H-Bond (Ligand Donor)	false
N04	N	MET- 95	2.87	166.64	H-Bond (Protein Donor)	false
C01	CD2	LEU- 129	4.39	0	Hydrophobic	false
C03	CD1	LEU- 129	4.49	0	Hydrophobic	false
C04	CG1	VAL- 134	4.42	0	Hydrophobic	false
C13	CD1	LEU- 145	3.83	0	Hydrophobic	false
C22	CD1	LEU- 145	3.41	0	Hydrophobic	false
C03	CG2	ILE- 154	4.46	0	Hydrophobic	false
C14	CB	ALA- 155	3.86	0	Hydrophobic	false
O01	N	ASP- 156	2.73	173.15	H-Bond (Protein Donor)	false
C03	CB	ASP- 156	3.98	0	Hydrophobic	false
C11	CG	LEU- 157	4.5	0	Hydrophobic	false
C13	CD1	LEU- 157	3.9	0	Hydrophobic	false