scPDB - 1ndh entry

Protein Data Bank Entry:

PDB ID : 1ndh

Resolution :2.100 Å

Experimental Method : X-ray

Deposition Date : 1994-10-31

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	NADH-cytochrome b5 reductase 3
ID:	NB5R3_PIG
AC:	P83686
Organism:	Sus scrofa
Reign:	Eukaryota
TaxID:	9823
EC Number:	1.6.2.2

Chains:

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

Ligand binding site composition:

B-Factor:	19.590
Number of residues:	39
Including
Standard Amino Acids:	38
Non Standard Amino Acids:	0
Water Molecules:	1
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.767	509.625

% Hydrophobic	% Polar
37.09	62.91
According to VolSite

Ligand :

HET Code:	FAD
Formula:	C27H31N9O15P2
Molecular weight:	783.534 g/mol
DrugBank ID:	DB03147
Buried Surface Area:	54.52 %
Polar Surface area:	381.7 Å2

Number of
H-Bond Acceptors:	22
H-Bond Donors:	7
Rings:	6
Aromatic rings:	3
Anionic atoms:	2
Cationic atoms:	0
Rule of Five Violation:	3
Rotatable Bonds:	13

Mass center Coordinates

X	Y	Z
9.40315	18.2082	-4.225

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
C7M	CB	HIS- 49	4.42	0	Hydrophobic	false
O1A	NH2	ARG- 63	3.33	120.81	H-Bond (Protein Donor)	false
O1A	NE	ARG- 63	3.31	124.59	H-Bond (Protein Donor)	false
O1P	NH2	ARG- 63	3.48	124.37	H-Bond (Protein Donor)	false
O1P	NE	ARG- 63	2.86	140.09	H-Bond (Protein Donor)	false
O1A	CZ	ARG- 63	3.64	0	Ionic (Protein Cationic)	false
O1P	CZ	ARG- 63	3.56	0	Ionic (Protein Cationic)	false
C3'	CB	ARG- 63	4.21	0	Hydrophobic	false
C9	CG	PRO- 64	3.9	0	Hydrophobic	false
C8M	CG	PRO- 64	3.42	0	Hydrophobic	false
O4'	OH	TYR- 65	2.52	147.63	H-Bond (Protein Donor)	false
C3'	CE1	TYR- 65	3.26	0	Hydrophobic	false
N5	N	THR- 66	3.48	162.35	H-Bond (Protein Donor)	false
C6	CB	THR- 66	4.4	0	Hydrophobic	false
N3	O	ILE- 81	2.67	169.35	H-Bond (Ligand Donor)	false
O2	N	VAL- 83	3.09	166.65	H-Bond (Protein Donor)	false
C5'	CE1	PHE- 85	4.38	0	Hydrophobic	false
C2B	CE2	PHE- 85	3.78	0	Hydrophobic	false
N6A	O	LYS- 86	3.04	129.46	H-Bond (Ligand Donor)	false
O2A	N	LYS- 97	2.55	168.59	H-Bond (Protein Donor)	false
O1P	N	MET- 98	2.86	158.04	H-Bond (Protein Donor)	false
O2P	OG	SER- 99	2.68	171.32	H-Bond (Protein Donor)	false
O2P	N	SER- 99	2.88	161.63	H-Bond (Protein Donor)	false
C1'	CB	THR- 153	4.14	0	Hydrophobic	false
O4	OG1	THR- 156	3.45	135.27	H-Bond (Protein Donor)	false
C6	CG2	THR- 156	4.1	0	Hydrophobic	false
O4	O	HOH- 284	2.55	159.31	H-Bond (Protein Donor)	false