scPDB - 1lc3 entry

Protein Data Bank Entry:

PDB ID : 1lc3

Resolution :1.500 Å

Experimental Method : X-ray

Deposition Date : 2002-04-05

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Biliverdin reductase A
ID:	BIEA_RAT
AC:	P46844
Organism:	Rattus norvegicus
Reign:	Eukaryota
TaxID:	10116
EC Number:	1.3.1.24

Chains:

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

Ligand binding site composition:

B-Factor:	15.657
Number of residues:	36
Including
Standard Amino Acids:	33
Non Standard Amino Acids:	0
Water Molecules:	3
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.473	708.750

% Hydrophobic	% Polar
41.90	58.10
According to VolSite

Ligand :

HET Code:	NAD
Formula:	C21H26N7O14P2
Molecular weight:	662.417 g/mol
DrugBank ID:	-
Buried Surface Area:	51.87 %
Polar Surface area:	343.54 Å2

Number of
H-Bond Acceptors:	18
H-Bond Donors:	6
Rings:	5
Aromatic rings:	3
Anionic atoms:	2
Cationic atoms:	1
Rule of Five Violation:	3
Rotatable Bonds:	11

Mass center Coordinates

X	Y	Z
30.9488	20.1251	59.4589

Binding mode :

What is Poseview ?

2D View
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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
O1A	N	ARG- 18	3.08	164.91	H-Bond (Protein Donor)	false
O2N	N	ALA- 19	2.72	165.61	H-Bond (Protein Donor)	false
O3D	OG	SER- 76	2.99	160.66	H-Bond (Protein Donor)	false
C4D	CB	GLU- 96	4.49	0	Hydrophobic	false
O2D	O	TYR- 97	2.72	166.5	H-Bond (Ligand Donor)	false
C5N	CE2	TYR- 97	3.34	0	Hydrophobic	false
C1B	CD1	LEU- 156	4.29	0	Hydrophobic	false
C5B	CZ	PHE- 161	4.2	0	Hydrophobic	false
C5D	CE2	PHE- 161	3.97	0	Hydrophobic	false
C3D	CD2	PHE- 161	4.18	0	Hydrophobic	false
N6A	O	SER- 167	2.85	170.37	H-Bond (Ligand Donor)	false
O2N	O	HOH- 1005	2.79	179.98	H-Bond (Protein Donor)	false
N1A	O	HOH- 1025	2.9	179.96	H-Bond (Protein Donor)	false