scPDB - 1sdu entry

Protein Data Bank Entry:

PDB ID : 1sdu

Resolution :1.250 Å

Experimental Method : X-ray

Deposition Date : 2004-02-14

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Gag-Pol polyprotein
ID:	POL_HV1BR
AC:	P03367
Organism:	Human immunodeficiency virus type 1 group M subtype B
Reign:	Viruses
TaxID:	11686
EC Number:	3.4.23.16

Chains:

Chain Name:	Percentage of Residues within binding site
A	51 %
B	49 %

Ligand binding site composition:

B-Factor:	11.245
Number of residues:	43
Including
Standard Amino Acids:	43
Non Standard Amino Acids:	0
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.955	685.125

% Hydrophobic	% Polar
47.78	52.22
According to VolSite

Ligand :

HET Code:	MK1
Formula:	C36H48N5O4
Molecular weight:	614.797 g/mol
DrugBank ID:	DB00224
Buried Surface Area:	68.17 %
Polar Surface area:	119.23 Å2

Number of
H-Bond Acceptors:	6
H-Bond Donors:	5
Rings:	5
Aromatic rings:	3
Anionic atoms:	0
Cationic atoms:	1
Rule of Five Violation:	1
Rotatable Bonds:	12

Mass center Coordinates

X	Y	Z
20.8073	30.951	13.8617

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
C16	CD2	LEU- 23	3.82	0	Hydrophobic	false
O2	OD2	ASP- 25	2.53	156.99	H-Bond (Ligand Donor)	false
C5	CB	ALA- 28	4.33	0	Hydrophobic	false
C6	CB	ALA- 28	3.82	0	Hydrophobic	false
C5	CB	ASP- 30	4.07	0	Hydrophobic	false
C5	CG2	VAL- 32	4.1	0	Hydrophobic	false
C6	CG2	VAL- 32	4.07	0	Hydrophobic	false
C5	CD1	ILE- 47	4.36	0	Hydrophobic	false
C7	CD1	ILE- 47	3.81	0	Hydrophobic	false
C30	CD1	ILE- 50	3.92	0	Hydrophobic	false
C29	CD1	ILE- 50	3.83	0	Hydrophobic	false
C19	CG	PRO- 81	3.9	0	Hydrophobic	false
C18	CG2	VAL- 82	3.61	0	Hydrophobic	false
C6	CG2	ILE- 84	4.24	0	Hydrophobic	false
C14	CD1	ILE- 84	3.73	0	Hydrophobic	false
N5	NH2	ARG- 108	3.07	140.92	H-Bond (Protein Donor)	false
O2	OD1	ASP- 125	2.66	157.63	H-Bond (Protein Donor)	false
N4	O	GLY- 127	3.2	164.55	H-Bond (Ligand Donor)	false
O4	O	GLY- 127	3.34	162.61	H-Bond (Ligand Donor)	false
C29	CB	ALA- 128	3.62	0	Hydrophobic	false
O4	N	ASP- 129	2.98	158.41	H-Bond (Protein Donor)	false
C26	CB	ASP- 130	3.72	0	Hydrophobic	false
C28	CG1	VAL- 132	3.79	0	Hydrophobic	false
C27	CD1	ILE- 147	3.79	0	Hydrophobic	false
C6	CG1	ILE- 150	4.29	0	Hydrophobic	false
C7	CG2	ILE- 150	4.03	0	Hydrophobic	false
C14	CG1	ILE- 150	4.39	0	Hydrophobic	false
C36	CB	PRO- 181	3.77	0	Hydrophobic	false
C32	CG1	VAL- 182	4.46	0	Hydrophobic	false
C28	CD1	ILE- 184	3.95	0	Hydrophobic	false