scPDB - 4nmd entry

Protein Data Bank Entry:

PDB ID : 4nmd

Resolution :1.980 Å

Experimental Method : X-ray

Deposition Date : 2013-11-14

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Bifunctional protein PutA
ID:	Q746X3_GEOSL
AC:	Q746X3
Organism:	Geobacter sulfurreducens
Reign:	Bacteria
TaxID:	243231
EC Number:	/

Chains:

Chain Name:	Percentage of Residues within binding site
A	98 %
B	2 %

Ligand binding site composition:

B-Factor:	24.519
Number of residues:	54
Including
Standard Amino Acids:	50
Non Standard Amino Acids:	0
Water Molecules:	4
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.085	874.125

% Hydrophobic	% Polar
52.90	47.10
According to VolSite

Ligand :

HET Code:	FDA
Formula:	C27H33N9O15P2
Molecular weight:	785.550 g/mol
DrugBank ID:	-
Buried Surface Area:	72.15 %
Polar Surface area:	381.04 Å2

Number of
H-Bond Acceptors:	21
H-Bond Donors:	9
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
66.6159	6.91857	-8.71817

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
N3	O	MET- 245	2.71	150	H-Bond (Ligand Donor)	false
O4	N	MET- 245	3.26	152.89	H-Bond (Protein Donor)	false
O2	NE2	GLN- 276	2.63	166.23	H-Bond (Protein Donor)	false
C2B	CD2	TYR- 278	4.16	0	Hydrophobic	false
C6	CD	ARG- 303	3.65	0	Hydrophobic	false
C6	CG1	VAL- 305	4.36	0	Hydrophobic	false
C2'	CB	VAL- 305	3.88	0	Hydrophobic	false
C9A	CG1	VAL- 305	3.73	0	Hydrophobic	false
O1A	NZ	LYS- 306	2.85	0	Ionic (Protein Cationic)	false
O1P	NZ	LYS- 306	2.94	0	Ionic (Protein Cationic)	false
C4B	CB	LYS- 306	4.08	0	Hydrophobic	false
O1P	NZ	LYS- 306	2.94	140.79	H-Bond (Protein Donor)	false
O3B	O	GLY- 307	2.96	166.5	H-Bond (Ligand Donor)	false
O2B	O	GLY- 307	2.73	144.82	H-Bond (Ligand Donor)	false
O2'	N	GLY- 307	2.84	127.18	H-Bond (Protein Donor)	false
O2	N	ALA- 308	2.93	147.32	H-Bond (Protein Donor)	false
C1'	CB	ALA- 308	4.21	0	Hydrophobic	false
C2B	CB	TRP- 310	4.37	0	Hydrophobic	false
N6A	O	THR- 328	3.04	157.88	H-Bond (Ligand Donor)	false
O1A	NZ	LYS- 330	2.92	179.32	H-Bond (Protein Donor)	false
O1A	NZ	LYS- 330	2.92	0	Ionic (Protein Cationic)	false
O2A	NZ	LYS- 330	3.86	0	Ionic (Protein Cationic)	false
C1B	CG	LYS- 330	4.33	0	Hydrophobic	false
C1B	CB	SER- 333	4.31	0	Hydrophobic	false
N3A	OG	SER- 333	2.74	160.07	H-Bond (Protein Donor)	false
C9	CB	ALA- 356	4.39	0	Hydrophobic	false
C8	CB	ALA- 356	3.73	0	Hydrophobic	false
O2P	ND1	HIS- 358	3	153.93	H-Bond (Protein Donor)	false
O2P	N	HIS- 358	2.95	161.3	H-Bond (Protein Donor)	false
O1A	ND2	ASN- 359	2.64	154.58	H-Bond (Protein Donor)	false
C7M	CB	GLN- 383	3.53	0	Hydrophobic	false
C8M	CG	LEU- 385	3.91	0	Hydrophobic	false
C7	CD2	LEU- 385	3.76	0	Hydrophobic	false
C8	CD2	LEU- 385	3.64	0	Hydrophobic	false
C7M	CB	TYR- 406	3.6	0	Hydrophobic	false
O2A	N	PHE- 432	3.12	178.53	H-Bond (Protein Donor)	false
O3B	O	HOH- 1543	3.48	123.29	H-Bond (Ligand Donor)	false