scPDB - 4xyb entry

Protein Data Bank Entry:

PDB ID : 4xyb

Resolution :1.380 Å

Experimental Method : X-ray

Deposition Date : 2015-02-02

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Formate dehydrogenase
ID:	G8NVB5_GRAMM
AC:	G8NVB5
Organism:	Granulicella mallensis
Reign:	Bacteria
TaxID:	682795
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	9.366
Number of residues:	56
Including
Standard Amino Acids:	52
Non Standard Amino Acids:	0
Water Molecules:	4
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.033	506.250

% Hydrophobic	% Polar
50.00	50.00
According to VolSite

Ligand :

HET Code:	NDP
Formula:	C21H26N7O17P3
Molecular weight:	741.389 g/mol
DrugBank ID:	DB02338
Buried Surface Area:	71.49 %
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
-6.47875	3.22635	-10.6349

Binding mode :

What is Poseview ?

2D View
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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
C5N	CB	ILE- 123	3.52	0	Hydrophobic	false
C3D	CG2	ILE- 123	3.94	0	Hydrophobic	false
C5N	CG2	VAL- 151	3.74	0	Hydrophobic	false
C4N	CG2	VAL- 151	3.4	0	Hydrophobic	false
C4B	CB	ALA- 199	3.69	0	Hydrophobic	false
C1B	CB	ALA- 199	3.57	0	Hydrophobic	false
O1A	N	ARG- 202	2.96	168.48	H-Bond (Protein Donor)	false
O1A	NH1	ARG- 202	2.86	147.64	H-Bond (Protein Donor)	false
O1A	CZ	ARG- 202	3.84	0	Ionic (Protein Cationic)	false
O1N	N	ILE- 203	2.8	171.73	H-Bond (Protein Donor)	false
C5D	CD1	ILE- 203	4.2	0	Hydrophobic	false
C5N	CD1	ILE- 203	3.83	0	Hydrophobic	false
O1X	NE	ARG- 223	3.43	126.56	H-Bond (Protein Donor)	false
O1X	NH2	ARG- 223	2.86	141.56	H-Bond (Protein Donor)	false
O2X	N	ARG- 223	2.87	156.77	H-Bond (Protein Donor)	false
O2X	NE	ARG- 223	2.77	171.75	H-Bond (Protein Donor)	false
O1X	CZ	ARG- 223	3.54	0	Ionic (Protein Cationic)	false
O2X	CZ	ARG- 223	3.67	0	Ionic (Protein Cationic)	false
O3X	N	HIS- 224	3.19	148.6	H-Bond (Protein Donor)	false
C5B	CG	PRO- 257	3.88	0	Hydrophobic	false
N7A	OH	TYR- 259	2.67	174.62	H-Bond (Protein Donor)	false
N6A	OH	TYR- 259	3.1	161.32	H-Bond (Ligand Donor)	false
N7N	O	THR- 283	2.94	167.98	H-Bond (Ligand Donor)	false
N7N	OD1	ASP- 309	3.2	136.13	H-Bond (Ligand Donor)	false
N7N	OD2	ASP- 309	3.16	162.64	H-Bond (Ligand Donor)	false
O7N	NE2	HIS- 333	2.86	142.52	H-Bond (Protein Donor)	false
O7N	N	GLY- 336	3.04	133.67	H-Bond (Protein Donor)	false
O2A	OG	SER- 381	2.61	160.06	H-Bond (Protein Donor)	false
C5B	CB	SER- 381	4.3	0	Hydrophobic	false
C3B	CB	SER- 381	4.38	0	Hydrophobic	false
O1N	O	HOH- 639	2.73	179.95	H-Bond (Protein Donor)	false
O2D	O	HOH- 651	2.86	154.78	H-Bond (Ligand Donor)	false