scPDB - 4ivg entry

Protein Data Bank Entry:

PDB ID : 4ivg

Resolution :1.750 Å

Experimental Method : X-ray

Deposition Date : 2013-01-22

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	TNF receptor-associated protein 1
ID:	A8WFV1_DANRE
AC:	A8WFV1
Organism:	Danio rerio
Reign:	Eukaryota
TaxID:	7955
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	36.825
Number of residues:	44
Including
Standard Amino Acids:	41
Non Standard Amino Acids:	1
Water Molecules:	2
Cofactors:
Metals:	MG

Cavity properties

Ligandability	Volume (Å3)
0.112	627.750

% Hydrophobic	% Polar
38.71	61.29
According to VolSite

Ligand :

HET Code:	ANP
Formula:	C10H13N6O12P3
Molecular weight:	502.164 g/mol
DrugBank ID:	-
Buried Surface Area:	72.75 %
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
-15.1922	3.07706	-26.3635

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
O1A	ND2	ASN- 134	2.91	138.09	H-Bond (Protein Donor)	false
N6	OD2	ASP- 173	2.89	161.65	H-Bond (Ligand Donor)	false
C1'	SD	MET- 178	3.83	0	Hydrophobic	false
C4'	CB	ASN- 186	3.79	0	Hydrophobic	false
C1'	CB	ASN- 186	4.1	0	Hydrophobic	false
O1B	OG	SER- 193	2.55	152.62	H-Bond (Protein Donor)	false
O3'	N	GLY- 194	2.85	161.44	H-Bond (Protein Donor)	false
O3G	N	GLN- 215	2.74	166.43	H-Bond (Protein Donor)	false
O3G	N	PHE- 216	2.95	178.4	H-Bond (Protein Donor)	false
O1G	N	VAL- 218	2.9	156.62	H-Bond (Protein Donor)	false
O1G	N	GLY- 219	2.82	148.47	H-Bond (Protein Donor)	false
O2A	N	PHE- 220	2.93	168.46	H-Bond (Protein Donor)	false
N1	OG1	THR- 266	3.43	136.31	H-Bond (Protein Donor)	false
O3G	NH2	ARG- 417	2.71	166.9	H-Bond (Protein Donor)	false
O3G	NE	ARG- 417	3.39	131.78	H-Bond (Protein Donor)	false
O3G	CZ	ARG- 417	3.48	0	Ionic (Protein Cationic)	false
O2G	MG	MG- 803	2.06	0	Metal Acceptor	false
O2B	MG	MG- 803	2.16	0	Metal Acceptor	false
O1A	MG	MG- 803	2.12	0	Metal Acceptor	false
N1	O	HOH- 901	2.76	155.62	H-Bond (Protein Donor)	false
O1G	O	HOH- 919	2.85	179.97	H-Bond (Protein Donor)	false