scPDB - 2h63 entry

Protein Data Bank Entry:

PDB ID : 2h63

Resolution :2.700 Å

Experimental Method : X-ray

Deposition Date : 2006-05-30

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_HUMAN
AC:	P53004
Organism:	Homo sapiens
Reign:	Eukaryota
TaxID:	9606
EC Number:	1.3.1.24

Chains:

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

Ligand binding site composition:

B-Factor:	71.075
Number of residues:	32
Including
Standard Amino Acids:	32
Non Standard Amino Acids:	0
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.789	1144.125

% Hydrophobic	% Polar
42.77	57.23
According to VolSite

Ligand :

HET Code:	NAP
Formula:	C21H25N7O17P3
Molecular weight:	740.381 g/mol
DrugBank ID:	DB03461
Buried Surface Area:	56.06 %
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
7.95431	3.36287	23.9148

Binding mode :

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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
O2X	N	VAL- 16	3.1	155.5	H-Bond (Protein Donor)	false
O1A	NH1	ARG- 18	3.49	136.41	H-Bond (Protein Donor)	false
O2A	N	ARG- 18	2.67	171.8	H-Bond (Protein Donor)	false
O2A	NH1	ARG- 18	3.46	164.69	H-Bond (Protein Donor)	false
O1N	CZ	ARG- 18	3.5	0	Ionic (Protein Cationic)	false
O2N	N	ALA- 19	2.83	166.32	H-Bond (Protein Donor)	false
C5D	CB	ALA- 19	4.28	0	Hydrophobic	false
O2X	OG	SER- 44	2.67	160.7	H-Bond (Protein Donor)	false
O3X	CZ	ARG- 45	3.05	0	Ionic (Protein Cationic)	false
O3X	N	ARG- 45	2.67	165.14	H-Bond (Protein Donor)	false
N1A	NH1	ARG- 46	3.35	121.98	H-Bond (Protein Donor)	false
O2X	NH2	ARG- 46	2.99	144.7	H-Bond (Protein Donor)	false
O2X	NE	ARG- 46	3.37	131.85	H-Bond (Protein Donor)	false
O1X	CZ	ARG- 46	3.28	0	Ionic (Protein Cationic)	false
O2X	CZ	ARG- 46	3.57	0	Ionic (Protein Cationic)	false
DuAr	CZ	ARG- 46	3.64	16.41	Pi/Cation	false
C4B	CG	GLU- 76	4.29	0	Hydrophobic	false
O3D	OG	SER- 77	3.26	163.1	H-Bond (Ligand Donor)	false
C4D	CB	GLU- 97	4.18	0	Hydrophobic	false
O2D	O	TYR- 98	2.86	160.43	H-Bond (Ligand Donor)	false
C5N	CE2	TYR- 98	3.46	0	Hydrophobic	false
C3D	CE1	PHE- 162	4.44	0	Hydrophobic	false
C2D	CD1	PHE- 162	4.39	0	Hydrophobic	false