scPDB - 1hbm entry

Protein Data Bank Entry:

PDB ID : 1hbm

Resolution :1.800 Å

Experimental Method : X-ray

Deposition Date : 2001-04-20

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Methyl-coenzyme M reductase I subunit alpha	Methyl-coenzyme M reductase I subunit beta
ID:	MCRA_METTM	MCRB_METTM
AC:	P11558	P11560
Organism:	Methanothermobacter marburgensis
Reign:	Archaea
TaxID:	79929
EC Number:	2.8.4.1

Chains:

Chain Name:	Percentage of Residues within binding site
A	18 %
D	50 %
E	32 %

Ligand binding site composition:

B-Factor:	10.999
Number of residues:	42
Including
Standard Amino Acids:	38
Non Standard Amino Acids:	4
Water Molecules:	0
Cofactors:
Metals:	NA

Cavity properties

Ligandability	Volume (Å3)
0.381	550.125

% Hydrophobic	% Polar
53.37	46.63
According to VolSite

Ligand :

HET Code:	SHT
Formula:	C13H20NO10PS3
Molecular weight:	477.467 g/mol
DrugBank ID:	-
Buried Surface Area:	80.04 %
Polar Surface area:	267.64 Å2

Number of
H-Bond Acceptors:	12
H-Bond Donors:	1
Rings:	0
Aromatic rings:	0
Anionic atoms:	4
Cationic atoms:	0
Rule of Five Violation:	1
Rotatable Bonds:	15

Mass center Coordinates

X	Y	Z
24.7493	38.0717	-48.0738

Binding mode :

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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
OXT	CZ	ARG- 225	3.36	0	Ionic (Protein Cationic)	false
O	CZ	ARG- 225	3.88	0	Ionic (Protein Cationic)	false
OXT	NE	ARG- 225	2.62	165.07	H-Bond (Protein Donor)	false
OXT	NH1	ARG- 225	3.28	127.27	H-Bond (Protein Donor)	false
O	NH1	ARG- 225	3.01	168.58	H-Bond (Protein Donor)	false
OXT	NZ	LYS- 256	2.93	172.22	H-Bond (Protein Donor)	false
O8P	NZ	LYS- 256	2.72	158.03	H-Bond (Protein Donor)	false
OXT	NZ	LYS- 256	2.93	0	Ionic (Protein Cationic)	false
O8P	NZ	LYS- 256	2.72	0	Ionic (Protein Cationic)	false
CB	CD	ARG- 270	4.27	0	Hydrophobic	false
O1P	NH2	ARG- 270	2.77	162.15	H-Bond (Protein Donor)	false
O1P	CZ	ARG- 270	3.75	0	Ionic (Protein Cationic)	false
CK3	CD2	LEU- 320	4.15	0	Hydrophobic	false
CK1	CE	MET- 324	4.32	0	Hydrophobic	false
CK3	CB	MET- 324	3.99	0	Hydrophobic	false
CK4	CB	SER- 325	3.74	0	Hydrophobic	false
S1	CZ	PHE- 330	3.67	0	Hydrophobic	false
CC	CE1	PHE- 330	3.59	0	Hydrophobic	false
CK6	CE2	PHE- 330	3.64	0	Hydrophobic	false
CK3	CE2	PHE- 330	4.44	0	Hydrophobic	false
CK4	CZ	PHE- 330	3.9	0	Hydrophobic	false
OS3	OH	TYR- 333	2.78	168.69	H-Bond (Protein Donor)	false
S1	CE2	TYR- 333	3.82	0	Hydrophobic	false
SK	CZ	PHE- 361	4.01	0	Hydrophobic	false
CK5	CZ	PHE- 361	4.26	0	Hydrophobic	false
CD	CZ	PHE- 361	3.94	0	Hydrophobic	false
CG2	CE2	PHE- 362	3.76	0	Hydrophobic	false
CK1	CZ	PHE- 362	3.89	0	Hydrophobic	false
OS1	OH	TYR- 367	2.59	137.86	H-Bond (Protein Donor)	false
CD	CE1	TYR- 367	4.28	0	Hydrophobic	false
CC	CZ	TYR- 367	3.69	0	Hydrophobic	false
CK4	CD2	TYR- 367	3.63	0	Hydrophobic	false
O2P	N	GLY- 369	2.82	150.71	H-Bond (Protein Donor)	false
CG2	CG2	ILE- 380	3.69	0	Hydrophobic	false
CG2	CG2	VAL- 381	3.8	0	Hydrophobic	false
S1	CE2	PHE- 443	3.96	0	Hydrophobic	false
CD	CD1	PHE- 443	3.36	0	Hydrophobic	false
SK	CZ	PHE- 443	3.32	0	Hydrophobic	false
SK	CB	ASN- 481	4.32	0	Hydrophobic	false
S1	CG2	VAL- 482	3.39	0	Hydrophobic	false
CK6	CG1	VAL- 482	4.27	0	Hydrophobic	false