scPDB - 2cnd entry

Protein Data Bank Entry:

PDB ID : 2cnd

Resolution :2.500 Å

Experimental Method : X-ray

Deposition Date : 1995-02-01

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Nitrate reductase [NADH]
ID:	NIA1_MAIZE
AC:	P17571
Organism:	Zea mays
Reign:	Eukaryota
TaxID:	4577
EC Number:	1.7.1.1

Chains:

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

Ligand binding site composition:

B-Factor:	30.900
Number of residues:	36
Including
Standard Amino Acids:	36
Non Standard Amino Acids:	0
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.930	519.750

% Hydrophobic	% Polar
38.31	61.69
According to VolSite

Ligand :

HET Code:	FAD
Formula:	C27H31N9O15P2
Molecular weight:	783.534 g/mol
DrugBank ID:	DB03147
Buried Surface Area:	58.5 %
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
17.9532	17.3683	4.76198

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- 48	4.45	0	Hydrophobic	false
O2A	CZ	ARG- 62	3.39	0	Ionic (Protein Cationic)	false
O2P	CZ	ARG- 62	3.63	0	Ionic (Protein Cationic)	false
O2P	NH1	ARG- 62	2.72	161.22	H-Bond (Protein Donor)	false
C3'	CG	ARG- 62	3.67	0	Hydrophobic	false
C8	CB	ALA- 63	3.66	0	Hydrophobic	false
C2'	CE1	TYR- 64	4.42	0	Hydrophobic	false
O4	N	THR- 65	3.43	156.93	H-Bond (Protein Donor)	false
C6	CB	THR- 65	4.42	0	Hydrophobic	false
N3	O	LEU- 79	2.7	160.17	H-Bond (Ligand Donor)	false
O2	N	LYS- 81	3.08	162.19	H-Bond (Protein Donor)	false
C5B	CE2	TYR- 83	4.1	0	Hydrophobic	false
C1B	CD2	TYR- 83	4.42	0	Hydrophobic	false
C5'	CD2	TYR- 83	3.68	0	Hydrophobic	false
C2B	CE2	TYR- 83	3.35	0	Hydrophobic	false
N6A	O	PHE- 84	2.95	158.04	H-Bond (Ligand Donor)	false
C1B	CG	PHE- 91	3.43	0	Hydrophobic	false
O1A	N	LEU- 96	3.04	167.5	H-Bond (Protein Donor)	false
O2P	N	MET- 97	2.88	137.23	H-Bond (Protein Donor)	false
O1P	N	THR- 98	2.99	149.71	H-Bond (Protein Donor)	false
C5'	CG2	THR- 98	4.11	0	Hydrophobic	false
N1	OG	SER- 146	3.36	124.58	H-Bond (Protein Donor)	false
C6	CG	PRO- 150	3.86	0	Hydrophobic	false
C7M	CB	PHE- 270	4.14	0	Hydrophobic	false