scPDB - 1nmk entry

Protein Data Bank Entry:

PDB ID : 1nmk

Resolution :2.100 Å

Experimental Method : X-ray

Deposition Date : 2003-01-10

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Peptidyl-prolyl cis-trans isomerase A
ID:	PPIA_HUMAN
AC:	P62937
Organism:	Homo sapiens
Reign:	Eukaryota
TaxID:	9606
EC Number:	5.2.1.8

Chains:

Chain Name:	Percentage of Residues within binding site
A	11 %
B	89 %

Ligand binding site composition:

B-Factor:	17.658
Number of residues:	32
Including
Standard Amino Acids:	28
Non Standard Amino Acids:	1
Water Molecules:	3
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.661	533.250

% Hydrophobic	% Polar
44.94	55.06
According to VolSite

Ligand :

HET Code:	SFM
Formula:	C39H56N4O10
Molecular weight:	740.883 g/mol
DrugBank ID:	-
Buried Surface Area:	47.48 %
Polar Surface area:	214.82 Å2

Number of
H-Bond Acceptors:	11
H-Bond Donors:	7
Rings:	3
Aromatic rings:	1
Anionic atoms:	0
Cationic atoms:	0
Rule of Five Violation:	3
Rotatable Bonds:	8

Mass center Coordinates

X	Y	Z
28.7678	2.34526	54.0832

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
O66	NH2	ARG- 55	3.2	140.75	H-Bond (Protein Donor)	false
O72	NH1	ARG- 55	3.3	157.23	H-Bond (Protein Donor)	false
O69	NH2	ARG- 55	3.3	148.66	H-Bond (Protein Donor)	false
C23	CD1	ILE- 57	3.97	0	Hydrophobic	false
C3	CE1	PHE- 60	3.82	0	Hydrophobic	false
C23	CE1	PHE- 60	4.15	0	Hydrophobic	false
C49	CE1	PHE- 60	3.59	0	Hydrophobic	false
C26	CD1	PHE- 60	3.89	0	Hydrophobic	false
C3	CE	MET- 61	4.18	0	Hydrophobic	false
N65	OE1	GLN- 63	3	149.17	H-Bond (Ligand Donor)	false
O69	NE2	GLN- 63	3.01	164.49	H-Bond (Protein Donor)	false
C54	CB	THR- 73	4.1	0	Hydrophobic	false
C57	CB	ALA- 101	4.03	0	Hydrophobic	false
N9	O	ASN- 102	2.83	157.1	H-Bond (Ligand Donor)	false
O67	N	ASN- 102	2.92	156.88	H-Bond (Protein Donor)	false
C57	CB	GLN- 111	3.99	0	Hydrophobic	false
C4	CE1	PHE- 113	3.76	0	Hydrophobic	false
C58	CD2	TRP- 121	4.04	0	Hydrophobic	false
C50	CE2	TRP- 121	4.16	0	Hydrophobic	false
C49	CH2	TRP- 121	3.46	0	Hydrophobic	false
C4	CD2	LEU- 122	4.33	0	Hydrophobic	false
O68	NE2	HIS- 126	2.65	151.88	H-Bond (Ligand Donor)	false
O69	O	HOH- 2001	2.81	179.96	H-Bond (Protein Donor)	false