scPDB - 4yt5 entry

Protein Data Bank Entry:

PDB ID : 4yt5

Resolution :1.900 Å

Experimental Method : X-ray

Deposition Date : 2015-03-17

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	H(2)-forming methylenetetrahydromethanopterin dehydrogenase-related protein MJ1338
ID:	HMDY_METJA
AC:	Q58734
Organism:	Methanocaldococcus jannaschii
Reign:	Archaea
TaxID:	243232
EC Number:	/

Chains:

Chain Name:	Percentage of Residues within binding site
A	70 %
B	30 %

Ligand binding site composition:

B-Factor:	48.186
Number of residues:	44
Including
Standard Amino Acids:	43
Non Standard Amino Acids:	0
Water Molecules:	1
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.730	961.875

% Hydrophobic	% Polar
60.70	39.30
According to VolSite

Ligand :

HET Code:	H4M
Formula:	C31H42N6O16P
Molecular weight:	785.670 g/mol
DrugBank ID:	DB03481
Buried Surface Area:	39.16 %
Polar Surface area:	354.26 Å2

Number of
H-Bond Acceptors:	21
H-Bond Donors:	8
Rings:	5
Aromatic rings:	1
Anionic atoms:	3
Cationic atoms:	0
Rule of Five Violation:	3
Rotatable Bonds:	17

Mass center Coordinates

X	Y	Z
22.8822	-31.2293	-9.53646

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
C16	CD2	LEU- 24	4.13	0	Hydrophobic	false
C9M	CE1	TYR- 25	3.57	0	Hydrophobic	false
C9M	CD1	LEU- 29	3.98	0	Hydrophobic	false
CX5	CB	PRO- 101	4.37	0	Hydrophobic	false
CX3	CB	PHE- 102	4.06	0	Hydrophobic	false
OX3	N	PHE- 102	2.7	163.65	H-Bond (Protein Donor)	false
C10	SG	CYS- 127	3.97	0	Hydrophobic	false
C13	CB	CYS- 127	4.26	0	Hydrophobic	false
C6	CG2	VAL- 159	3.43	0	Hydrophobic	false
C9M	CG2	VAL- 159	3.43	0	Hydrophobic	false
NA2	O	ALA- 212	3.26	136.11	H-Bond (Ligand Donor)	false
N3	O	ALA- 212	2.83	158.43	H-Bond (Ligand Donor)	false
C9	SD	MET- 214	4.28	0	Hydrophobic	false
C10	CG	MET- 214	4.05	0	Hydrophobic	false
C14	SD	MET- 214	3.83	0	Hydrophobic	false
C11	CE	MET- 214	4.31	0	Hydrophobic	false
C15	CG2	ILE- 237	3.39	0	Hydrophobic	false
CX3	CG	PRO- 240	4.42	0	Hydrophobic	false
CX5	CG	PRO- 240	4.47	0	Hydrophobic	false
CX1	SD	MET- 243	3.92	0	Hydrophobic	false
C12	CE	MET- 243	3.8	0	Hydrophobic	false
NA2	OG	SER- 279	3.01	130.83	H-Bond (Ligand Donor)	false
NA2	O	SER- 279	2.88	157.69	H-Bond (Ligand Donor)	false
N8	O	SER- 282	3.03	140.08	H-Bond (Ligand Donor)	false
C7	CE	MET- 283	3.35	0	Hydrophobic	false