scPDB - 3iqf entry

Protein Data Bank Entry:

PDB ID : 3iqf

Resolution :2.100 Å

Experimental Method : X-ray

Deposition Date : 2009-08-20

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	F420-dependent methylenetetrahydromethanopterin dehydrogenase
ID:	MTD_METKA
AC:	P94951
Organism:	Methanopyrus kandleri
Reign:	Archaea
TaxID:	190192
EC Number:	1.5.98.1

Chains:

Chain Name:	Percentage of Residues within binding site
H	18 %
L	82 %

Ligand binding site composition:

B-Factor:	25.233
Number of residues:	40
Including
Standard Amino Acids:	39
Non Standard Amino Acids:	0
Water Molecules:	1
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.570	803.250

% Hydrophobic	% Polar
60.92	39.08
According to VolSite

Ligand :

HET Code:	E4M
Formula:	C31H41N6O16P
Molecular weight:	784.662 g/mol
DrugBank ID:	-
Buried Surface Area:	51.17 %
Polar Surface area:	354.03 Å2

Number of
H-Bond Acceptors:	20
H-Bond Donors:	8
Rings:	5
Aromatic rings:	1
Anionic atoms:	3
Cationic atoms:	1
Rule of Five Violation:	3
Rotatable Bonds:	17

Mass center Coordinates

X	Y	Z
39.1661	-22.5395	80.7066

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
N1	ND2	ASN- 13	3.13	161.79	H-Bond (Protein Donor)	false
C13	CB	ARG- 27	4.04	0	Hydrophobic	false
C9M	CB	ALA- 28	3.71	0	Hydrophobic	false
C7M	CG1	VAL- 42	3.56	0	Hydrophobic	false
C9M	CB	VAL- 42	4.41	0	Hydrophobic	false
C10	CG	MET- 124	4.45	0	Hydrophobic	false
C16	SD	MET- 124	3.88	0	Hydrophobic	false
C7	CD2	LEU- 125	4.25	0	Hydrophobic	false
C10	CD1	LEU- 125	3.85	0	Hydrophobic	false
OH4	N	LEU- 125	3.3	159.8	H-Bond (Protein Donor)	false
CX2	CB	ALA- 127	4.31	0	Hydrophobic	false
C13	CB	ALA- 127	3.51	0	Hydrophobic	false
OX2	O	ALA- 127	2.74	166.31	H-Bond (Ligand Donor)	false
O4J	NH2	ARG- 128	3.43	124.67	H-Bond (Protein Donor)	false
OX5	NH2	ARG- 128	2.97	139.96	H-Bond (Protein Donor)	false
C3J	CD	ARG- 128	4.32	0	Hydrophobic	false
CX5	CD	ARG- 128	4.02	0	Hydrophobic	false
O2J	N	ARG- 129	2.98	148.98	H-Bond (Protein Donor)	false
O3J	N	ARG- 129	3.12	136.28	H-Bond (Protein Donor)	false
C2J	CB	ARG- 129	4.04	0	Hydrophobic	false
O3J	OE2	GLU- 130	2.64	162.15	H-Bond (Ligand Donor)	false
C7	CG	MET- 137	3.95	0	Hydrophobic	false
N1	ND2	ASN- 141	2.96	153.77	H-Bond (Protein Donor)	false
NA2	OD1	ASN- 141	2.77	159.03	H-Bond (Ligand Donor)	false
CX2	CB	CYS- 221	4.4	0	Hydrophobic	false
CX1	CE1	PHE- 222	3.95	0	Hydrophobic	false
CX3	CE1	PHE- 222	4.21	0	Hydrophobic	false
C4J	CZ	TYR- 230	4.33	0	Hydrophobic	false
O2J	O	HOH- 305	2.86	149.13	H-Bond (Ligand Donor)	false