scPDB - 1civ entry

Protein Data Bank Entry:

PDB ID : 1civ

Resolution :2.800 Å

Experimental Method : X-ray

Deposition Date : 1999-04-01

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Malate dehydrogenase [NADP], chloroplastic
ID:	MDHP_FLABI
AC:	P46489
Organism:	Flaveria bidentis
Reign:	Eukaryota
TaxID:	4224
EC Number:	1.1.1.82

Chains:

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

Ligand binding site composition:

B-Factor:	22.689
Number of residues:	59
Including
Standard Amino Acids:	56
Non Standard Amino Acids:	0
Water Molecules:	3
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.930	479.250

% Hydrophobic	% Polar
47.89	52.11
According to VolSite

Ligand :

HET Code:	NAP
Formula:	C21H25N7O17P3
Molecular weight:	740.381 g/mol
DrugBank ID:	DB03461
Buried Surface Area:	64.24 %
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
5.8589	114.573	45.3936

Binding mode :

What is Poseview ?

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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
N3A	N	GLY- 49	3.36	130.82	H-Bond (Protein Donor)	false
O3X	N	ALA- 51	2.84	151.02	H-Bond (Protein Donor)	false
O1A	N	MET- 53	2.65	125.36	H-Bond (Protein Donor)	false
C5N	CD1	ILE- 54	3.75	0	Hydrophobic	false
O2X	N	SER- 81	3.08	123.84	H-Bond (Protein Donor)	false
O2X	OG	SER- 81	3.02	157.25	H-Bond (Protein Donor)	false
C4D	CB	ALA- 127	4.44	0	Hydrophobic	false
C3N	CG2	VAL- 167	4.45	0	Hydrophobic	false
O4D	N	ASN- 169	3.47	142.82	H-Bond (Protein Donor)	false
O3D	N	ASN- 169	3.1	134.24	H-Bond (Protein Donor)	false
O2D	ND2	ASN- 169	2.69	166.83	H-Bond (Protein Donor)	false
C2D	CB	ASN- 169	4.04	0	Hydrophobic	false
N7N	O	LEU- 193	3.26	166.67	H-Bond (Ligand Donor)	false
C4N	CD1	LEU- 196	4.42	0	Hydrophobic	false
C4N	CG2	THR- 280	3.65	0	Hydrophobic	false
C2D	CG	GLU- 384	4.39	0	Hydrophobic	false
C5N	CG	GLU- 384	3.88	0	Hydrophobic	false
O2D	OXT	MET- 385	2.79	156.37	H-Bond (Ligand Donor)	false
O1A	O	HOH- 394	2.71	179.95	H-Bond (Protein Donor)	false