scPDB - 1dap entry

Protein Data Bank Entry:

PDB ID : 1dap

Resolution :2.200 Å

Experimental Method : X-ray

Deposition Date : 1996-07-08

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Meso-diaminopimelate D-dehydrogenase
ID:	DAPDH_CORGL
AC:	P04964
Organism:	Corynebacterium glutamicum
Reign:	Bacteria
TaxID:	196627
EC Number:	1.4.1.16

Chains:

Chain Name:	Percentage of Residues within binding site
B	100 %

Ligand binding site composition:

B-Factor:	21.024
Number of residues:	53
Including
Standard Amino Acids:	47
Non Standard Amino Acids:	0
Water Molecules:	6
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.420	857.250

% Hydrophobic	% Polar
37.01	62.99
According to VolSite

Ligand :

HET Code:	NDP
Formula:	C21H26N7O17P3
Molecular weight:	741.389 g/mol
DrugBank ID:	DB02338
Buried Surface Area:	65.55 %
Polar Surface area:	404.9 Å2

Number of
H-Bond Acceptors:	22
H-Bond Donors:	5
Rings:	5
Aromatic rings:	2
Anionic atoms:	4
Cationic atoms:	0
Rule of Five Violation:	2
Rotatable Bonds:	13

Mass center Coordinates

X	Y	Z
17.8963	22.2239	38.8899

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
O2X	N	TYR- 11	2.93	157.14	H-Bond (Protein Donor)	false
O1A	N	ASN- 13	2.85	156.05	H-Bond (Protein Donor)	false
O1N	ND2	ASN- 13	3.33	158.47	H-Bond (Protein Donor)	false
O2N	N	LEU- 14	2.73	177.59	H-Bond (Protein Donor)	false
C5D	CB	LEU- 14	4.28	0	Hydrophobic	false
O2X	OG	SER- 35	2.59	153.9	H-Bond (Protein Donor)	false
O3X	OG	SER- 35	3.47	131.03	H-Bond (Protein Donor)	false
O2B	NH2	ARG- 36	2.86	160.41	H-Bond (Protein Donor)	false
O3X	N	ARG- 36	2.89	173.23	H-Bond (Protein Donor)	false
O3X	NE	ARG- 36	2.96	165.59	H-Bond (Protein Donor)	false
O3X	CZ	ARG- 36	3.75	0	Ionic (Protein Cationic)	false
O1X	NE	ARG- 37	2.69	165.34	H-Bond (Protein Donor)	false
O2X	NH2	ARG- 37	3.1	158.93	H-Bond (Protein Donor)	false
O1X	CZ	ARG- 37	3.57	0	Ionic (Protein Cationic)	false
O2X	CZ	ARG- 37	3.82	0	Ionic (Protein Cationic)	false
DuAr	CZ	ARG- 37	3.82	154.25	Pi/Cation	false
O3B	O	CYS- 65	3.05	149.93	H-Bond (Ligand Donor)	false
O3D	N	SER- 68	2.94	144.22	H-Bond (Protein Donor)	false
O2D	OG	SER- 68	3.13	167.6	H-Bond (Protein Donor)	false
C3N	CB	THR- 88	4.04	0	Hydrophobic	false
N7N	O	THR- 88	3	169.96	H-Bond (Ligand Donor)	false
O7N	N	TRP- 119	2.79	141.23	H-Bond (Protein Donor)	false
O7N	N	ASP- 120	3.12	151.82	H-Bond (Protein Donor)	false
N7N	O	PRO- 121	3.15	153.08	H-Bond (Ligand Donor)	false
O1N	NE2	GLN- 150	2.9	170.86	H-Bond (Protein Donor)	false
O5D	NE2	GLN- 150	3.47	123.31	H-Bond (Protein Donor)	false
C5N	CB	GLN- 150	3.95	0	Hydrophobic	false
C2D	CB	GLN- 150	4.14	0	Hydrophobic	false
C4N	CG2	THR- 274	3.41	0	Hydrophobic	false
O2A	O	HOH- 420	2.92	179.97	H-Bond (Protein Donor)	false
O3D	O	HOH- 421	2.92	157.29	H-Bond (Ligand Donor)	false
O2N	O	HOH- 422	2.93	172.32	H-Bond (Protein Donor)	false
O1N	O	HOH- 425	2.75	179.97	H-Bond (Protein Donor)	false