scPDB - 1lwi entry

Protein Data Bank Entry:

PDB ID : 1lwi

Resolution :2.700 Å

Experimental Method : X-ray

Deposition Date : 1996-02-24

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	3-alpha-hydroxysteroid dehydrogenase
ID:	DIDH_RAT
AC:	P23457
Organism:	Rattus norvegicus
Reign:	Eukaryota
TaxID:	10116
EC Number:	1.1.1.50

Chains:

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

Ligand binding site composition:

B-Factor:	29.000
Number of residues:	41
Including
Standard Amino Acids:	41
Non Standard Amino Acids:	0
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.283	1161.000

% Hydrophobic	% Polar
44.48	55.52
According to VolSite

Ligand :

HET Code:	NAP
Formula:	C21H25N7O17P3
Molecular weight:	740.381 g/mol
DrugBank ID:	DB03461
Buried Surface Area:	63.74 %
Polar Surface area:	405.54 Å2

Number of
H-Bond Acceptors:	21
H-Bond Donors:	5
Rings:	5
Aromatic rings:	3
Anionic atoms:	4
Cationic atoms:	1
Rule of Five Violation:	2
Rotatable Bonds:	13

Mass center Coordinates

X	Y	Z
-15.1609	-22.9793	51.561

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
C3D	CB	THR- 24	4.26	0	Hydrophobic	false
O3D	OG1	THR- 24	3.32	170.99	H-Bond (Ligand Donor)	false
O2D	OD2	ASP- 50	2.75	156.42	H-Bond (Ligand Donor)	false
C2D	CE2	TYR- 55	3.96	0	Hydrophobic	false
N7N	OG	SER- 166	2.98	161.2	H-Bond (Ligand Donor)	false
O7N	ND2	ASN- 167	3.06	164.9	H-Bond (Protein Donor)	false
N7N	OE1	GLN- 190	2.74	168.37	H-Bond (Ligand Donor)	false
C3N	CB	TYR- 216	4.38	0	Hydrophobic	false
C5N	CB	TYR- 216	4.3	0	Hydrophobic	false
DuAr	DuAr	TYR- 216	3.77	0	Aromatic Face/Face	false
O1A	N	LEU- 219	3.2	133.83	H-Bond (Protein Donor)	false
O1A	N	SER- 221	2.59	131.98	H-Bond (Protein Donor)	false
O2N	OG	SER- 221	3.08	169.73	H-Bond (Protein Donor)	false
C5D	CB	ARG- 270	3.72	0	Hydrophobic	false
O1X	OG	SER- 271	3.18	159.44	H-Bond (Protein Donor)	false
O2X	CZ	ARG- 276	3.25	0	Ionic (Protein Cationic)	false
O3X	CZ	ARG- 276	3.21	0	Ionic (Protein Cationic)	false
N6A	OE1	GLU- 279	3.24	169.56	H-Bond (Ligand Donor)	false