scPDB - 1i36 entry

Protein Data Bank Entry:

PDB ID : 1i36

Resolution :2.000 Å

Experimental Method : X-ray

Deposition Date : 2001-02-13

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Conserved protein
ID:	O27779_METTH
AC:	O27779
Organism:	Methanothermobacter thermautotrophicus
Reign:	Archaea
TaxID:	187420
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	26.185
Number of residues:	41
Including
Standard Amino Acids:	38
Non Standard Amino Acids:	0
Water Molecules:	3
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.798	378.000

% Hydrophobic	% Polar
44.64	55.36
According to VolSite

Ligand :

HET Code:	NAP
Formula:	C21H25N7O17P3
Molecular weight:	740.381 g/mol
DrugBank ID:	DB03461
Buried Surface Area:	53.51 %
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
55.4082	37.2917	55.3159

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
O2A	N	GLU- 10	2.97	175.02	H-Bond (Protein Donor)	false
N7N	OE1	GLU- 10	3.5	158.41	H-Bond (Ligand Donor)	false
O2N	N	VAL- 11	2.8	169.84	H-Bond (Protein Donor)	false
C3N	CG2	VAL- 11	3.84	0	Hydrophobic	false
C5D	CG2	VAL- 11	3.93	0	Hydrophobic	false
O2B	NE	ARG- 33	3.11	133.57	H-Bond (Protein Donor)	false
O2X	NE	ARG- 33	3.17	155.02	H-Bond (Protein Donor)	false
DuAr	CZ	ARG- 33	3.51	171.02	Pi/Cation	false
C1B	CD	ARG- 33	4.38	0	Hydrophobic	false
O1X	OG	SER- 34	2.84	165.55	H-Bond (Protein Donor)	false
O2X	N	SER- 34	2.62	167.76	H-Bond (Protein Donor)	false
O3B	OG1	THR- 37	2.97	157.3	H-Bond (Ligand Donor)	false
O1X	OG1	THR- 37	2.61	143.13	H-Bond (Protein Donor)	false
C5D	CB	ALA- 63	4.2	0	Hydrophobic	false
C5B	CG2	THR- 65	4.27	0	Hydrophobic	false
C3D	CB	ASN- 88	4.42	0	Hydrophobic	false
O3D	OD1	ASN- 88	2.89	173.33	H-Bond (Ligand Donor)	false
O3D	N	ASN- 89	3.31	149.54	H-Bond (Protein Donor)	false
O2D	N	ASN- 89	3.36	143.05	H-Bond (Protein Donor)	false
C2D	CB	ASN- 89	4.36	0	Hydrophobic	false
C5N	CB	ILE- 112	3.82	0	Hydrophobic	false
C4N	CD1	ILE- 112	4.11	0	Hydrophobic	false
C3N	CG2	VAL- 116	4.04	0	Hydrophobic	false
O2N	O	HOH- 1365	2.75	179.96	H-Bond (Protein Donor)	false
N1A	O	HOH- 1376	3.18	179.95	H-Bond (Protein Donor)	false