scPDB - 2cwf entry

Protein Data Bank Entry:

PDB ID : 2cwf

Resolution :1.800 Å

Experimental Method : X-ray

Deposition Date : 2005-06-20

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Delta(1)-pyrroline-2-carboxylate/Delta(1)-piperideine-2-carboxylate reductase
ID:	PY2CR_PSEUB
AC:	Q4U331
Organism:	Pseudomonas syringae pv. tomato
Reign:	Bacteria
TaxID:	323
EC Number:	/

Chains:

Chain Name:	Percentage of Residues within binding site
A	88 %
B	12 %

Ligand binding site composition:

B-Factor:	21.099
Number of residues:	50
Including
Standard Amino Acids:	48
Non Standard Amino Acids:	0
Water Molecules:	2
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.023	1248.750

% Hydrophobic	% Polar
37.84	62.16
According to VolSite

Ligand :

HET Code:	NDP
Formula:	C21H26N7O17P3
Molecular weight:	741.389 g/mol
DrugBank ID:	DB02338
Buried Surface Area:	60.35 %
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
28.9698	53.01	35.5841

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
O4D	NE2	HIS- 54	2.66	123.32	H-Bond (Protein Donor)	false
N7N	O	HIS- 126	3.31	140.56	H-Bond (Ligand Donor)	false
N7N	O	ALA- 128	2.95	151.12	H-Bond (Ligand Donor)	false
O2D	N	LEU- 130	3.15	134.89	H-Bond (Protein Donor)	false
C4N	CB	SER- 150	4.33	0	Hydrophobic	false
C5N	CB	THR- 166	3.62	0	Hydrophobic	false
C2D	CB	PRO- 168	4	0	Hydrophobic	false
C4N	CG	PRO- 168	3.73	0	Hydrophobic	false
O3B	N	ASP- 184	2.86	152.05	H-Bond (Protein Donor)	false
C3D	CB	ASP- 184	4.44	0	Hydrophobic	false
O3D	OD2	ASP- 184	2.58	173.39	H-Bond (Ligand Donor)	false
O2D	OD2	ASP- 184	2.9	148.68	H-Bond (Ligand Donor)	false
O2D	OD1	ASP- 184	2.62	140.16	H-Bond (Ligand Donor)	false
C5B	CB	LEU- 185	3.76	0	Hydrophobic	false
O1N	N	ALA- 186	2.92	171.62	H-Bond (Protein Donor)	false
C5N	CB	ALA- 186	4.1	0	Hydrophobic	false
O1A	NE2	HIS- 236	2.86	165.99	H-Bond (Protein Donor)	false
O1N	NZ	LYS- 237	3.23	0	Ionic (Protein Cationic)	false
O3X	NH2	ARG- 309	2.76	136.08	H-Bond (Protein Donor)	false
O3X	CZ	ARG- 309	3.95	0	Ionic (Protein Cationic)	false
C1B	CB	PRO- 311	4.39	0	Hydrophobic	false
O2X	N	GLY- 312	2.75	142.27	H-Bond (Protein Donor)	false
O3X	CZ	ARG- 314	3.8	0	Ionic (Protein Cationic)	false
O2N	O	HOH- 2564	2.72	179.98	H-Bond (Protein Donor)	false
O2X	O	HOH- 2767	2.66	169.72	H-Bond (Protein Donor)	false