scPDB - 5bsg entry

Protein Data Bank Entry:

PDB ID : 5bsg

Resolution :1.950 Å

Experimental Method : X-ray

Deposition Date : 2015-06-02

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Pyrroline-5-carboxylate reductase
ID:	G7KRM5_MEDTR
AC:	G7KRM5
Organism:	Medicago truncatula
Reign:	Eukaryota
TaxID:	3880
EC Number:	/

Chains:

Chain Name:	Percentage of Residues within binding site
I	3 %
J	97 %

Ligand binding site composition:

B-Factor:	44.515
Number of residues:	40
Including
Standard Amino Acids:	37
Non Standard Amino Acids:	0
Water Molecules:	3
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.409	1329.750

% Hydrophobic	% Polar
48.48	51.52
According to VolSite

Ligand :

HET Code:	NAP
Formula:	C21H25N7O17P3
Molecular weight:	740.381 g/mol
DrugBank ID:	DB03461
Buried Surface Area:	58.32 %
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
39.6734	29.9647	30.4289

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
O1A	N	LYS- 20	3.08	169.02	H-Bond (Protein Donor)	false
O1N	NZ	LYS- 20	2.95	163.88	H-Bond (Protein Donor)	false
O2A	NZ	LYS- 20	3.66	0	Ionic (Protein Cationic)	false
O1N	NZ	LYS- 20	2.95	0	Ionic (Protein Cationic)	false
O2N	N	MET- 21	2.89	172.06	H-Bond (Protein Donor)	false
C5D	CB	MET- 21	4.38	0	Hydrophobic	false
C3N	CE	MET- 21	3.26	0	Hydrophobic	false
O1X	ND1	HIS- 45	3.18	142.12	H-Bond (Protein Donor)	false
C1B	CB	HIS- 45	4.2	0	Hydrophobic	false
O1X	N	SER- 46	2.98	159.29	H-Bond (Protein Donor)	false
O1X	OG	SER- 46	2.74	167.19	H-Bond (Protein Donor)	false
O1X	N	ASN- 47	3.45	155.85	H-Bond (Protein Donor)	false
N1A	ND2	ASN- 65	2.96	175.67	H-Bond (Protein Donor)	false
C1B	CG1	VAL- 79	4.45	0	Hydrophobic	false
O3D	O	VAL- 79	2.76	170.99	H-Bond (Ligand Donor)	false
O2A	NZ	LYS- 80	3.04	150.97	H-Bond (Protein Donor)	false
O2A	NZ	LYS- 80	3.04	0	Ionic (Protein Cationic)	false
C3D	CD	LYS- 80	4.41	0	Hydrophobic	false
C4D	CG2	VAL- 104	4.08	0	Hydrophobic	false
O2D	N	ALA- 106	3.19	153.35	H-Bond (Protein Donor)	false
C5N	CE	MET- 126	3.83	0	Hydrophobic	false
C5N	CG	PRO- 127	3.81	0	Hydrophobic	false
N3A	O	HOH- 447	3.15	179.99	H-Bond (Protein Donor)	false
O2N	O	HOH- 483	2.85	172.58	H-Bond (Protein Donor)	false