scPDB - 2c3c entry

Protein Data Bank Entry:

PDB ID : 2c3c

Resolution :2.150 Å

Experimental Method : X-ray

Deposition Date : 2005-10-05

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	2-oxopropyl-CoM reductase, carboxylating
ID:	XECC_XANP2
AC:	Q56839
Organism:	Xanthobacter autotrophicus
Reign:	Bacteria
TaxID:	78245
EC Number:	1.8.1.5

Chains:

Chain Name:	Percentage of Residues within binding site
A	6 %
B	94 %

Ligand binding site composition:

B-Factor:	23.044
Number of residues:	71
Including
Standard Amino Acids:	62
Non Standard Amino Acids:	1
Water Molecules:	8
Cofactors:	NAP
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.636	786.375

% Hydrophobic	% Polar
40.77	59.23
According to VolSite

Ligand :

HET Code:	FAD
Formula:	C27H31N9O15P2
Molecular weight:	783.534 g/mol
DrugBank ID:	DB03147
Buried Surface Area:	77.02 %
Polar Surface area:	381.7 Å2

Number of
H-Bond Acceptors:	22
H-Bond Donors:	7
Rings:	6
Aromatic rings:	3
Anionic atoms:	2
Cationic atoms:	0
Rule of Five Violation:	3
Rotatable Bonds:	13

Mass center Coordinates

X	Y	Z
64.223	-12.9642	27.6761

Binding mode :

What is Poseview ?

2D View
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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
O1P	N	ALA- 54	2.89	162.46	H-Bond (Protein Donor)	false
O3B	OD2	ASP- 73	3.07	157.78	H-Bond (Ligand Donor)	false
O3B	OD1	ASP- 73	2.52	128.5	H-Bond (Ligand Donor)	false
O2B	OD2	ASP- 73	3.02	138.74	H-Bond (Ligand Donor)	false
N3A	N	ARG- 74	3.19	148.09	H-Bond (Protein Donor)	false
C3B	CE3	TRP- 75	3.75	0	Hydrophobic	false
O2A	N	SER- 81	3.06	151.54	H-Bond (Protein Donor)	false
O2A	OG	SER- 81	3.08	176.75	H-Bond (Protein Donor)	false
C8	CB	ALA- 86	3.77	0	Hydrophobic	false
C9A	SG	CYS- 87	4.23	0	Hydrophobic	false
C2'	SG	CYS- 87	3.98	0	Hydrophobic	false
N5	ND1	HIS- 90	2.89	141.73	H-Bond (Protein Donor)	false
C6	CB	HIS- 90	4.05	0	Hydrophobic	false
O4	NE2	HIS- 91	2.97	151.36	H-Bond (Protein Donor)	false
N1A	N	ALA- 158	2.92	177.17	H-Bond (Protein Donor)	false
C7M	CB	HIS- 202	3.47	0	Hydrophobic	false
C7M	CG2	THR- 225	4.12	0	Hydrophobic	false
C7M	CE2	TYR- 229	3.68	0	Hydrophobic	false
C8M	CG	GLU- 314	4.18	0	Hydrophobic	false
O3'	OD2	ASP- 353	3.4	130.96	H-Bond (Ligand Donor)	false
O3'	OD1	ASP- 353	2.66	172.12	H-Bond (Ligand Donor)	false
C5'	CB	ASP- 353	4.31	0	Hydrophobic	false
O2P	N	ASP- 353	2.89	156.43	H-Bond (Protein Donor)	false
N1	N	MET- 361	3.37	131.74	H-Bond (Protein Donor)	false
O2	N	MET- 361	2.71	166	H-Bond (Protein Donor)	false
C4'	SD	MET- 361	3.76	0	Hydrophobic	false
C5'	CB	ALA- 364	3.97	0	Hydrophobic	false
N3	O	PHE- 501	2.85	148.62	H-Bond (Ligand Donor)	false
O3B	O	HOH- 2055	2.93	130.1	H-Bond (Protein Donor)	false
O2P	O	HOH- 2252	2.82	179.96	H-Bond (Protein Donor)	false
O1A	O	HOH- 2253	2.72	179.95	H-Bond (Protein Donor)	false
O2	O	HOH- 2364	2.72	179.95	H-Bond (Protein Donor)	false
O1A	O	HOH- 2365	2.62	179.96	H-Bond (Protein Donor)	false
O1P	O	HOH- 2366	2.68	170.18	H-Bond (Protein Donor)	false