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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 209 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 175 families.
1 4YMX Kd = 79 nM ARG C6 H15 N4 O2 C(C[C@@H](....
50% Homology Family (28)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 149 families.
1 1WDN Kd = 0.5 uM GLN C5 H10 N2 O3 C(CC(=O)N)....
2 4POW Kd = 0.57 uM OP1 C11 H18 N4 O5 [H]/N=C(N)....
3 5ITO Kd = 68.9 uM 6DB C9 H18 N4 O4 [H]/N=C(/N....
4 5ITP Kd = 6.1 uM 6DB C9 H18 N4 O4 [H]/N=C(/N....
5 4POX Kd = 3.7 uM 2W2 C11 H20 N4 O6 [H]/N=C(/N....
6 5OTA Kd = 4.4 uM AQQ C8 H16 N2 O4 C[C@H](C(=....
7 4PP0 - OP1 C11 H18 N4 O5 [H]/N=C(N)....
8 2Y7I - ARG C6 H15 N4 O2 C(C[C@@H](....
9 4G4P Kd = 0.13 uM GLN C5 H10 N2 O3 C(CC(=O)N)....
10 2PVU Kd = 0.49 uM LYS C6 H15 N2 O2 C(CC[NH3+]....
11 2Q2C Kd = 0.42 uM HIS C6 H10 N3 O2 c1c([nH+]c....
12 4YMX Kd = 79 nM ARG C6 H15 N4 O2 C(C[C@@H](....
13 1LST - LYS C6 H15 N2 O2 C(CC[NH3+]....
14 1LAF Kd = 14 nM ARG C6 H15 N4 O2 C(C[C@@H](....
15 5OWF Kd = 1.59 uM GLN C5 H10 N2 O3 C(CC(=O)N)....
16 1LAH Kd = 30 nM ORN C5 H12 N2 O2 C(C[C@@H](....
17 2PYY Kd = 0.2 uM GLU C5 H9 N O4 C(CC(=O)O)....
18 1HSL Kd = 0.064 uM HIS C6 H10 N3 O2 c1c([nH+]c....
19 1HPB Kd = 0.03 uM HIS C6 H10 N3 O2 c1c([nH+]c....
20 3VV5 - SLZ C5 H12 N2 O2 S C(CSC[C@@H....
21 3VVE - LYS C6 H15 N2 O2 C(CC[NH3+]....
22 3VVF - ARG C6 H15 N4 O2 C(C[C@@H](....
23 3VVD - ORN C5 H12 N2 O2 C(C[C@@H](....
24 5L9O Kd = 4 uM GOP C11 H22 N2 O8 C(CC(=O)N)....
25 4ZV1 Kd = 5.7 uM ARG C6 H15 N4 O2 C(C[C@@H](....
26 4ZV2 Kd = 1.2 mM GLN C5 H10 N2 O3 C(CC(=O)N)....
27 5ORG Kd = 9 nM 6DB C9 H18 N4 O4 [H]/N=C(/N....
28 4KQP Kd = 1.49 uM GLN C5 H10 N2 O3 C(CC(=O)N)....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: ARG; Similar ligands found: 42
No: Ligand ECFP6 Tc MDL keys Tc
1 ARG 1 1
2 DAR 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 4JK 0.585366 0.789474
8 NMM 0.585366 0.888889
9 VUR 0.585366 0.810811
10 HAR 0.585366 0.780488
11 VIO 0.581395 0.769231
12 WT2 0.571429 0.805556
13 DA2 0.55814 0.744186
14 2MR 0.545455 0.864865
15 2YH 0.545455 0.65
16 3KJ 0.545455 0.680851
17 1KJ 0.533333 0.744186
18 JM2 0.533333 0.731707
19 NRG 0.521739 0.622642
20 RPI 0.521739 0.64
21 2YJ 0.521739 0.619048
22 API 0.515152 0.611111
23 LN6 0.510638 0.725
24 HRG 0.5 0.941176
25 JM7 0.5 0.731707
26 2KJ 0.489796 0.727273
27 D20 0.489796 0.744186
28 AS1 0.489796 0.8
29 ORN 0.472222 0.757576
30 JM8 0.470588 0.714286
31 JM6 0.470588 0.697674
32 JM4 0.470588 0.697674
33 LYS ARG LYS ARG LYS ARG LYS ARG 0.463415 0.848485
34 MLZ 0.463415 0.65
35 JM5 0.461538 0.714286
36 DLY 0.447368 0.735294
37 DAB 0.441176 0.685714
38 LYS 0.435897 0.764706
39 0TF 0.428571 0.619048
40 2YG 0.42 0.619048
41 PG3 0.416667 0.756757
42 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 with APoc: 59
This union binding pocket(no: 1) in the query (biounit: 4ymx.bio2) has 16 residues
No: Leader PDB Ligand Sequence Similarity
1 1M13 HYF 1.53846
2 4WA2 SIA GAL NAG 2.69231
3 5O4J SAH 2.69231
4 5O4J 9KH 2.69231
5 1BZY IMU 2.76498
6 1G8S MET 3.04348
7 1QFY FAD 3.07692
8 1QFY NAP 3.07692
9 1OFD AKG 3.46154
10 4J7U YTZ 3.46154
11 4J7U NAP 3.46154
12 2HSA FMN 3.46154
13 3CTL S6P 3.4632
14 1G27 BB1 3.57143
15 6F7L CWH 3.84615
16 1KPH SAH 3.84615
17 4ETZ C2E 3.84615
18 1TPY SAH 3.84615
19 1CDO NAD 3.84615
20 4LO2 GAL BGC 4.08163
21 1VAY AZA 4.23077
22 1KPG SAH 4.23077
23 2H7C COA 4.23077
24 4PVR ASP 5
25 6H3O FAD 5
26 4DR9 BB2 5.20833
27 4ZU3 4SD 5.28634
28 1U7Z PMT 5.75221
29 2VVL FAD 6.15385
30 6CUZ FEV 6.53846
31 2NZ5 226 6.92308
32 3G5K BB2 7.10383
33 1NVM OXL 7.69231
34 2P3C 3TL 8.08081
35 2O4N TPV 8.08081
36 2ZQO NGA 9.23077
37 4ZDM GLY 10
38 4J56 FAD 10
39 1DQS NAD 14.6154
40 4YKI GLY 16.7969
41 4JWX 1N4 19.6154
42 5DT6 GLU 20.7692
43 5CMK GLU 20.8494
44 5O4F 8VE 21.3178
45 5IKB KAI 22.5681
46 4IO2 GLU 22.5806
47 5DEX GLY 23.4615
48 4WXJ GLU 29.6154
49 1II5 GLU 33.4764
50 3OEN GLU 33.8462
51 2RCA GLY 35.3846
52 5AA4 6X4 37.6923
53 3FV1 DYH 38.2812
54 5CC2 CKA 38.8462
55 2RC8 DSN 40.3846
56 4F2Q QUS 41.4729
57 1M5B BN1 41.5385
58 4C0R GDS 42.3387
59 6H1U ASP 45.7692
Pocket No.: 2; Query (leader) PDB : 4YMX; Ligand: ARG; Similar sites found with APoc: 8
This union binding pocket(no: 2) in the query (biounit: 4ymx.bio1) has 16 residues
No: Leader PDB Ligand Sequence Similarity
1 4DDS 0J7 2.30769
2 2J1P GRG 3.46154
3 3C3N FMN 5.76923
4 4M8X KGQ 6.06061
5 5MTE BB2 8.0292
6 1S17 GNR 8.88889
7 1LQY BB2 9.78261
8 2V6K TGG 9.81308
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