scPDB - 3t1a entry

Protein Data Bank Entry:

PDB ID : 3t1a

Resolution :2.400 Å

Experimental Method : X-ray

Deposition Date : 2011-07-21

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_HV1H2
AC:	P04585
Organism:	Human immunodeficiency virus type 1 group M subtype B
Reign:	Viruses
TaxID:	11706
EC Number:	2.7.7.49

Chains:

Chain Name:	Percentage of Residues within binding site
A	97 %
B	3 %

Ligand binding site composition:

B-Factor:	45.983
Number of residues:	34
Including
Standard Amino Acids:	34
Non Standard Amino Acids:	0
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.418	637.875

% Hydrophobic	% Polar
64.55	35.45
According to VolSite

Ligand :

HET Code:	5MA
Formula:	C20H15Cl3N7O
Molecular weight:	475.738 g/mol
DrugBank ID:	-
Buried Surface Area:	80.06 %
Polar Surface area:	109.15 Å2

Number of
H-Bond Acceptors:	5
H-Bond Donors:	2
Rings:	5
Aromatic rings:	5
Anionic atoms:	0
Cationic atoms:	1
Rule of Five Violation:	0
Rotatable Bonds:	5

Mass center Coordinates

X	Y	Z
8.69613	11.7288	17.0171

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
CL2	CB	PRO- 95	3.49	0	Hydrophobic	false
C2	CB	LEU- 100	4.47	0	Hydrophobic	false
C3	CD1	LEU- 100	4.09	0	Hydrophobic	false
C14	CB	LEU- 100	4.15	0	Hydrophobic	false
C6	CD2	LEU- 100	3.78	0	Hydrophobic	false
C2	CB	ASN- 103	4.33	0	Hydrophobic	false
N16	N	ASN- 103	3	174.02	H-Bond (Protein Donor)	false
N17	O	ASN- 103	2.85	157.54	H-Bond (Ligand Donor)	false
CL3	CG2	VAL- 106	3.85	0	Hydrophobic	false
C5	CG2	VAL- 106	3.76	0	Hydrophobic	false
C19	CG1	VAL- 106	3.98	0	Hydrophobic	false
C2	CG1	VAL- 106	3.64	0	Hydrophobic	false
CL3	CG2	VAL- 108	3.64	0	Hydrophobic	false
CL1	CB	VAL- 179	4.36	0	Hydrophobic	false
CL1	CD2	TYR- 181	3.43	0	Hydrophobic	false
CL2	CD1	TYR- 181	4.12	0	Hydrophobic	false
C6	CB	TYR- 181	4.32	0	Hydrophobic	false
CL1	CB	TYR- 188	3.99	0	Hydrophobic	false
CL2	CD1	TYR- 188	4.39	0	Hydrophobic	false
C5	CB	TYR- 188	4.4	0	Hydrophobic	false
C8	CB	TYR- 188	3.62	0	Hydrophobic	false
C7	CB	TYR- 188	3.25	0	Hydrophobic	false
C22	CB	PRO- 225	3.94	0	Hydrophobic	false
CL3	CD2	PHE- 227	3.59	0	Hydrophobic	false
CL2	CH2	TRP- 229	3.83	0	Hydrophobic	false
C23	CB	LEU- 234	4.45	0	Hydrophobic	false
C9	CD1	LEU- 234	3.47	0	Hydrophobic	false
C22	CG	PRO- 236	4.35	0	Hydrophobic	false
C14	CZ	TYR- 318	3.41	0	Hydrophobic	false