Receptor
PDB id Resolution Class Description Source Keywords
4YMX 1.48 Å NON-ENZYME: TRANSPORT CRYSTAL STRUCTURE OF THE SUBSTRATE BINDING PROTEIN OF AN AMI ABC TRANSPORTER CALDANAEROBACTER SUBTERRANEUS SUBSP. TENGCONGENSIS MB4 ABC TRANSPORTER TWO BINDING SITES SUBSTRATE SPECIFICITY MPROTEIN COMPLEX TRANSPORT PROTEIN
Ref.: STRUCTURAL BASIS FOR SUBSTRATE SPECIFICITY OF AN AM ABC TRANSPORTER PROC.NATL.ACAD.SCI.USA V. 112 5243 2015
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
ARG B:301;
A:301;
Valid;
Valid;
none;
none;
Kd = 79 nM
175.209 C6 H15 N4 O2 C(C[C...
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90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
4YMX 1.48 Å NON-ENZYME: TRANSPORT CRYSTAL STRUCTURE OF THE SUBSTRATE BINDING PROTEIN OF AN AMI ABC TRANSPORTER CALDANAEROBACTER SUBTERRANEUS SUBSP. TENGCONGENSIS MB4 ABC TRANSPORTER TWO BINDING SITES SUBSTRATE SPECIFICITY MPROTEIN COMPLEX TRANSPORT PROTEIN
Ref.: STRUCTURAL BASIS FOR SUBSTRATE SPECIFICITY OF AN AM ABC TRANSPORTER PROC.NATL.ACAD.SCI.USA V. 112 5243 2015
Members (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 199 families.
1 4YMX Kd = 79 nM ARG C6 H15 N4 O2 C(C[C@@H](....
70% Homology Family (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 166 families.
1 4YMX Kd = 79 nM ARG C6 H15 N4 O2 C(C[C@@H](....
50% Homology Family (9)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 141 families.
1 2Q2C Kd = 0.42 uM HIS C6 H10 N3 O2 c1c([nH+]c....
2 4YMX Kd = 79 nM ARG C6 H15 N4 O2 C(C[C@@H](....
3 1LST - LYS C6 H15 N2 O2 C(CC[NH3+]....
4 1LAF Kd = 14 nM ARG C6 H15 N4 O2 C(C[C@@H](....
5 3VV5 - SLZ C5 H12 N2 O2 S C(CSC[C@@H....
6 3VVE - LYS C6 H15 N2 O2 C(CC[NH3+]....
7 3VVF - ARG C6 H15 N4 O2 C(C[C@@H](....
8 3VVD - ORN C5 H12 N2 O2 C(C[C@@H](....
9 4ZV2 Kd = 1.2 mM GLN C5 H10 N2 O3 C(CC(=O)N)....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: ARG; Similar ligands found: 39
No: Ligand ECFP6 Tc MDL keys Tc
1 DAR 1 1
2 ARG 1 1
3 CIR 0.735294 0.763158
4 AAR 0.705882 0.783784
5 ILO 0.615385 0.783784
6 3AR 0.595238 0.891892
7 HAR 0.585366 0.780488
8 VUR 0.585366 0.810811
9 4JK 0.585366 0.789474
10 VIO 0.581395 0.769231
11 WT2 0.571429 0.805556
12 DA2 0.55814 0.744186
13 3KJ 0.545455 0.680851
14 2YH 0.545455 0.65
15 1KJ 0.533333 0.744186
16 JM2 0.533333 0.731707
17 2YJ 0.521739 0.619048
18 NRG 0.521739 0.622642
19 RPI 0.521739 0.64
20 API 0.515152 0.611111
21 LN6 0.510638 0.725
22 JM7 0.5 0.731707
23 HRG 0.5 0.941176
24 D20 0.489796 0.744186
25 AS1 0.489796 0.8
26 2KJ 0.489796 0.727273
27 ORN 0.472222 0.757576
28 JM6 0.470588 0.697674
29 JM4 0.470588 0.697674
30 JM8 0.470588 0.714286
31 MLZ 0.463415 0.65
32 JM5 0.461538 0.714286
33 DLY 0.447368 0.735294
34 DAB 0.441176 0.685714
35 LYS 0.435897 0.764706
36 0TF 0.428571 0.619048
37 2YG 0.42 0.619048
38 PG3 0.416667 0.756757
39 6CL 0.414634 0.638889
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 4YMX; Ligand: ARG; Similar sites found: 27
This union binding pocket(no: 1) in the query (biounit: 4ymx.bio2) has 16 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 1M13 HYF 0.02953 0.40437 1.53846
2 4WA2 SIA GAL NAG 0.0131 0.40745 2.69231
3 1QFY NAP 0.04297 0.40113 3.07692
4 1QFY FAD 0.04297 0.40113 3.07692
5 2HSA FMN 0.03095 0.40097 3.46154
6 1KPH SAH 0.01558 0.40762 3.84615
7 4ETZ C2E 0.009614 0.4064 3.84615
8 1KPG SAH 0.01669 0.40615 4.23077
9 4PVR ASP 0.007665 0.41551 5
10 4DR9 BB2 0.005837 0.41912 5.20833
11 1U7Z PMT 0.03922 0.40019 5.75221
12 2O4N TPV 0.02065 0.40598 8.08081
13 4J56 FAD 0.0456 0.4067 10
14 1DQS NAD 0.03728 0.40805 14.6154
15 4JWX 1N4 0.0076 0.41613 19.6154
16 5DT6 GLU 0.001332 0.42107 20.7692
17 5O4F 8VE 0.008501 0.40897 21.3178
18 5IKB KAI 0.004017 0.42225 22.5681
19 4IO2 GLU 0.00002211 0.53149 22.5806
20 5DEX GLY 0.0004795 0.43702 23.4615
21 4WXJ GLU 0.00575 0.40506 29.6154
22 3OEN GLU 0.002122 0.43267 33.8462
23 5AA4 6X4 0.00001952 0.407 37.6923
24 1M5B BN1 0.02762 0.44534 41.5385
25 4C0R GDS 0.0000009184 0.61734 42.3387
26 4POW OP1 0.000001306 0.49599 43.4615
27 2PYY GLU 0.00005663 0.49746 47.807
Pocket No.: 2; Query (leader) PDB : 4YMX; Ligand: ARG; Similar sites found: 2
This union binding pocket(no: 2) in the query (biounit: 4ymx.bio1) has 16 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 1S17 GNR 0.01021 0.41144 8.88889
2 1LQY BB2 0.01373 0.40333 9.78261
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