scPDB - 2w13 entry

Protein Data Bank Entry:

PDB ID : 2w13

Resolution :1.140 Å

Experimental Method : X-ray

Deposition Date : 2008-10-14

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Snake venom metalloproteinase BaP1
ID:	VM1B1_BOTAS
AC:	P83512
Organism:	Bothrops asper
Reign:	Eukaryota
TaxID:	8722
EC Number:	3.4.24

Chains:

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

Ligand binding site composition:

B-Factor:	5.198
Number of residues:	29
Including
Standard Amino Acids:	27
Non Standard Amino Acids:	1
Water Molecules:	1
Cofactors:
Metals:	ZN

Cavity properties

Ligandability	Volume (Å3)
0.240	246.375

% Hydrophobic	% Polar
36.99	63.01
According to VolSite

Ligand :

HET Code:	WR2
Formula:	C20H33N5O5S
Molecular weight:	455.572 g/mol
DrugBank ID:	DB08733
Buried Surface Area:	54.87 %
Polar Surface area:	177.76 Å2

Number of
H-Bond Acceptors:	6
H-Bond Donors:	5
Rings:	1
Aromatic rings:	1
Anionic atoms:	0
Cationic atoms:	0
Rule of Five Violation:	0
Rotatable Bonds:	11

Mass center Coordinates

X	Y	Z
10.7433	12.3075	21.6282

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
NAQ	O	ASN- 106	3.05	175.27	H-Bond (Ligand Donor)	false
CG1	CB	ASN- 106	3.95	0	Hydrophobic	false
OAG	OG1	THR- 107	2.62	160.64	H-Bond (Protein Donor)	false
OAJ	N	ILE- 108	2.82	167.63	H-Bond (Protein Donor)	false
CAC	CD1	ILE- 108	3.77	0	Hydrophobic	false
CBA	CG1	ILE- 108	3.74	0	Hydrophobic	false
NAR	O	GLY- 109	2.78	175.23	H-Bond (Ligand Donor)	false
SAU	CD	ARG- 110	3.96	0	Hydrophobic	false
DuAr	CZ	ARG- 110	3.5	12.56	Pi/Cation	false
CAC	CG2	THR- 139	4.02	0	Hydrophobic	false
CAC	CB	HIS- 142	4.3	0	Hydrophobic	false
OAK	OE1	GLU- 143	2.62	167.84	H-Bond (Protein Donor)	false
N	O	SER- 168	3.4	165.78	H-Bond (Ligand Donor)	false
CAF	CG2	VAL- 169	3.72	0	Hydrophobic	false
O	N	LEU- 170	3.07	169.53	H-Bond (Protein Donor)	false
CAB	CB	LEU- 170	4.34	0	Hydrophobic	false
OAI	ZN	ZN- 1203	2.01	0	Metal Acceptor	false
OAK	ZN	ZN- 1203	2.23	0	Metal Acceptor	false