scPDB - 4z3d entry

Protein Data Bank Entry:

PDB ID : 4z3d

Resolution :1.800 Å

Experimental Method : X-ray

Deposition Date : 2015-03-31

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Carbonyl reductase [NADPH] 1
ID:	CBR1_HUMAN
AC:	P16152
Organism:	Homo sapiens
Reign:	Eukaryota
TaxID:	9606
EC Number:	1.1.1.184

Chains:

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

Ligand binding site composition:

B-Factor:	17.613
Number of residues:	50
Including
Standard Amino Acids:	47
Non Standard Amino Acids:	0
Water Molecules:	3
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.191	968.625

% Hydrophobic	% Polar
44.95	55.05
According to VolSite

Ligand :

HET Code:	NDP
Formula:	C21H26N7O17P3
Molecular weight:	741.389 g/mol
DrugBank ID:	DB02338
Buried Surface Area:	78.57 %
Polar Surface area:	404.9 Å2

Number of
H-Bond Acceptors:	22
H-Bond Donors:	5
Rings:	5
Aromatic rings:	2
Anionic atoms:	4
Cationic atoms:	0
Rule of Five Violation:	2
Rotatable Bonds:	13

Mass center Coordinates

X	Y	Z
-11.6102	-39.1382	-40.7102

Binding mode :

What is Poseview ?

2D View
3D View

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	ND2	ASN- 13	2.94	173.74	H-Bond (Protein Donor)	false
C3B	CG	LYS- 14	3.91	0	Hydrophobic	false
O2X	NZ	LYS- 14	3.89	0	Ionic (Protein Cationic)	false
O2N	N	ILE- 16	2.85	157.25	H-Bond (Protein Donor)	false
C5D	CB	ILE- 16	4.14	0	Hydrophobic	false
C4D	CD1	ILE- 16	4.46	0	Hydrophobic	false
C3N	CD1	ILE- 16	4.18	0	Hydrophobic	false
O1X	NE	ARG- 37	2.87	169.7	H-Bond (Protein Donor)	false
O3X	NH1	ARG- 37	2.84	162.6	H-Bond (Protein Donor)	false
O1X	CZ	ARG- 37	3.73	0	Ionic (Protein Cationic)	false
O3X	CZ	ARG- 37	3.66	0	Ionic (Protein Cationic)	false
O1X	NH2	ARG- 41	2.79	157.69	H-Bond (Protein Donor)	false
O1X	NE	ARG- 41	3.38	131.8	H-Bond (Protein Donor)	false
O2X	NE	ARG- 41	3.39	127.49	H-Bond (Protein Donor)	false
O1X	CZ	ARG- 41	3.5	0	Ionic (Protein Cationic)	false
N6A	OD1	ASP- 62	3.18	140.88	H-Bond (Ligand Donor)	false
N1A	N	ILE- 63	3.02	162.33	H-Bond (Protein Donor)	false
O3D	O	ASN- 89	2.74	153.93	H-Bond (Ligand Donor)	false
C1B	CB	ALA- 90	4.19	0	Hydrophobic	false
C4D	CG1	VAL- 137	3.84	0	Hydrophobic	false
C5N	CB	SER- 139	3.69	0	Hydrophobic	false
O2D	OH	TYR- 193	2.73	163.61	H-Bond (Ligand Donor)	false
O3D	NZ	LYS- 197	2.93	141.38	H-Bond (Protein Donor)	false
O2D	NZ	LYS- 197	2.85	136.61	H-Bond (Protein Donor)	false
C5N	SG	CYS- 226	4.01	0	Hydrophobic	false
C5N	CG	PRO- 227	3.52	0	Hydrophobic	false
O7N	N	VAL- 230	2.79	170.36	H-Bond (Protein Donor)	false
N7N	O	VAL- 230	3.29	149.87	H-Bond (Ligand Donor)	false
O1N	OG1	THR- 232	2.68	171.06	H-Bond (Protein Donor)	false
C3D	CE	MET- 234	4.27	0	Hydrophobic	false
C2D	SD	MET- 234	3.71	0	Hydrophobic	false
O1A	O	HOH- 431	2.58	179.97	H-Bond (Protein Donor)	false
O2N	O	HOH- 468	2.7	179.98	H-Bond (Protein Donor)	false