scPDB - 5d3q entry

Protein Data Bank Entry:

PDB ID : 5d3q

Resolution :1.700 Å

Experimental Method : X-ray

Deposition Date : 2015-08-06

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Dynamin-1
ID:	DYN1_HUMAN
AC:	Q05193
Organism:	Homo sapiens
Reign:	Eukaryota
TaxID:	9606
EC Number:	3.6.5.5

Chains:

Chain Name:	Percentage of Residues within binding site
A	89 %
B	11 %

Ligand binding site composition:

B-Factor:	19.461
Number of residues:	37
Including
Standard Amino Acids:	36
Non Standard Amino Acids:	0
Water Molecules:	1
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.298	1366.875

% Hydrophobic	% Polar
36.79	63.21
According to VolSite

Ligand :

HET Code:	GDP
Formula:	C10H12N5O11P2
Molecular weight:	440.177 g/mol
DrugBank ID:	DB04315
Buried Surface Area:	73.2 %
Polar Surface area:	276.39 Å2

Number of
H-Bond Acceptors:	14
H-Bond Donors:	4
Rings:	3
Aromatic rings:	1
Anionic atoms:	3
Cationic atoms:	0
Rule of Five Violation:	1
Rotatable Bonds:	6

Mass center Coordinates

X	Y	Z
12.1529	25.555	57.7753

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
O3B	N	SER- 41	2.92	140.45	H-Bond (Protein Donor)	false
C5'	CB	SER- 41	4.11	0	Hydrophobic	false
O1B	N	GLY- 43	2.95	154.92	H-Bond (Protein Donor)	false
O3A	N	GLY- 43	3.18	123.09	H-Bond (Protein Donor)	false
O1B	N	LYS- 44	2.86	154.53	H-Bond (Protein Donor)	false
O2B	N	SER- 45	2.72	161.42	H-Bond (Protein Donor)	false
O2A	N	SER- 46	2.73	142.28	H-Bond (Protein Donor)	false
O2A	OG	SER- 46	2.58	151.3	H-Bond (Protein Donor)	false
C1'	CE	LYS- 206	4.23	0	Hydrophobic	false
O6	N	LYS- 206	2.88	136.3	H-Bond (Protein Donor)	false
N1	OD1	ASP- 208	2.84	159.5	H-Bond (Ligand Donor)	false
N2	OD1	ASP- 208	3.46	129.43	H-Bond (Ligand Donor)	false
N2	OD2	ASP- 208	2.88	161.02	H-Bond (Ligand Donor)	false
N2	OD1	ASP- 211	2.88	167.4	H-Bond (Ligand Donor)	false
N7	ND2	ASN- 236	3.01	162.01	H-Bond (Protein Donor)	false
O6	N	ASN- 236	2.77	167.02	H-Bond (Protein Donor)	false
O2'	O	ARG- 237	2.98	172.42	H-Bond (Ligand Donor)	false
O3'	OE1	GLN- 239	2.57	170.75	H-Bond (Ligand Donor)	false
C2'	CD1	ILE- 242	3.94	0	Hydrophobic	false