Receptor
PDB id Resolution Class Description Source Keywords
3KDM 1.5 Å NON-ENZYME: IMMUNE CRYSTAL STRUCTURE OF HUMAN ANTI-STEROID FAB 5F2 IN COMPLEX W TESTOSTERONE HOMO SAPIENS IMMUNE SYSTEM ANTIBODY IMMUNOGLOBULIN FAB FRAGMENT ANTI-S
Ref.: THE TESTOSTERONE BINDING MECHANISM OF AN ANTIBODY D FROM A NAIVE HUMAN SCFV LIBRARY J.MOL.RECOGNIT. V. 24 209 2010
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
TES B:226;
H:226;
Valid;
Valid;
none;
none;
Kd = 0.1 uM
288.424 C19 H28 O2 C[C@]...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
3KDM 1.5 Å NON-ENZYME: IMMUNE CRYSTAL STRUCTURE OF HUMAN ANTI-STEROID FAB 5F2 IN COMPLEX W TESTOSTERONE HOMO SAPIENS IMMUNE SYSTEM ANTIBODY IMMUNOGLOBULIN FAB FRAGMENT ANTI-S
Ref.: THE TESTOSTERONE BINDING MECHANISM OF AN ANTIBODY D FROM A NAIVE HUMAN SCFV LIBRARY J.MOL.RECOGNIT. V. 24 209 2010
Members (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 199 families.
1 3KDM Kd = 0.1 uM TES C19 H28 O2 C[C@]12CC[....
70% Homology Family (5)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1068 families.
1 3U7Y - FLC C6 H5 O7 C(C(=O)[O-....
2 3KDM Kd = 0.1 uM TES C19 H28 O2 C[C@]12CC[....
3 3LEV - ATP C10 H16 N5 O13 P3 c1nc(c2c(n....
4 4DVR - 0LY C17 H24 Br N3 O2 CC1(CC(CC(....
5 3PGF - GLC GLC n/a n/a
50% Homology Family (21)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 922 families.
1 3U7Y - FLC C6 H5 O7 C(C(=O)[O-....
2 1NC4 - DOF C23 H33 N5 O10 c1cc(ccc1C....
3 5DS8 - GLY 5CT GLY ALA n/a n/a
4 5DRN - 5CT C10 H23 N3 O3 C(CCNC[C@H....
5 3KDM Kd = 0.1 uM TES C19 H28 O2 C[C@]12CC[....
6 1QKZ - ALA ASN GLY GLY ALA SER GLY GLN VAL LYS n/a n/a
7 1NC2 - DOE C27 H41 N5 O10 S c1cc(ccc1C....
8 2HVK - TBA C16 H36 N CCCC[N+](C....
9 5DUB - GLY 5GG GLY ALA n/a n/a
10 5MES ic50 = 0.045 uM 7LT C44 H49 Cl2 N5 O4 CN1CCCN[C@....
11 1FE8 - NAG C8 H15 N O6 CC(=O)N[C@....
12 3LEV - ATP C10 H16 N5 O13 P3 c1nc(c2c(n....
13 5T85 - 44G C18 H35 O10 P CCCCCC(=O)....
14 1E4X Kd = 25 nM VAL VAL SER HIS PHE ASN ASP n/a n/a
15 4MA7 - P2Z C17 H20 N2 S CN(C)CCCN1....
16 4MA8 - Z80 C17 H19 Cl N2 S CN(C)CCCN1....
17 4DVR - 0LY C17 H24 Br N3 O2 CC1(CC(CC(....
18 4UUJ - XA7 C24 H52 N CCCCCC[N+]....
19 2DWE - TBA C16 H36 N CCCC[N+](C....
20 3PGF - GLC GLC n/a n/a
21 1MJJ Kd = 1.83 nM HAL C23 H29 N2 O7 P c1ccc(cc1)....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: TES; Similar ligands found: 10
No: Ligand ECFP6 Tc MDL keys Tc
1 FFA 1 1
2 TES 1 1
3 3G6 0.621622 0.868421
4 STR 0.619718 0.833333
5 1CA 0.6 0.785714
6 K2B 0.5625 0.763158
7 TH2 0.555556 0.829268
8 ASD 0.542857 0.833333
9 DL4 0.541176 0.85
10 6VW 0.405063 0.971429
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 3KDM; Ligand: TES; Similar sites found: 52
This union binding pocket(no: 1) in the query (biounit: 3kdm.bio1) has 12 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 5ISY NAD 0.01194 0.4099 2.22222
2 5LXC 7AA 0.02022 0.40187 3.11111
3 1K3A ACP 0.01674 0.40126 3.21101
4 3EE4 MYR 0.02223 0.40824 3.55556
5 5FLJ QUE 0.02406 0.40435 3.76344
6 4V03 ADP 0.01663 0.40445 4
7 2FCR FMN 0.01313 0.41375 4.04624
8 2IYA UDP 0.01973 0.40707 4.44444
9 4BCM T7Z 0.00518 0.43414 4.88889
10 1UM0 FMN 0.0112 0.4264 5.04587
11 3WWC BUA 0.006817 0.41254 5.04587
12 3NW7 LGV 0.02674 0.42497 5.33333
13 1PMO PLR 0.01289 0.4082 5.33333
14 3FW4 CAQ 0.02487 0.40825 5.61798
15 3VEH 0GA 0.02084 0.40284 5.77778
16 4K49 HFQ 0.03017 0.41363 5.88235
17 5TO8 7FM 0.008225 0.44686 5.9633
18 2YBQ SAH 0.02128 0.40494 5.9633
19 1VBO MAN MAN MAN 0.005051 0.41755 6.04027
20 3FJO FMN 0.006128 0.4393 6.42202
21 4ZSI 4R1 0.0111 0.41709 6.43275
22 4YHB FAD 0.02819 0.40794 6.66667
23 2AEL SAZ 0.0246 0.40215 6.66667
24 5KY3 GFB 0.02189 0.41158 6.88073
25 5UIU 8CG 0.03947 0.4035 6.88073
26 5W4W 9WG 0.03815 0.40259 7.55556
27 3DLS ADP 0.01126 0.40911 8
28 5LJI FMN 0.01661 0.41083 8.10811
29 5C8L GLC 0.02671 0.40562 8.24176
30 1TLL FMN 0.005276 0.45018 8.44444
31 5UR1 YY9 0.03054 0.4118 8.44444
32 3RI1 3RH 0.03066 0.41067 8.44444
33 5EYK 5U5 0.03522 0.40513 8.47458
34 5EOB 5QQ 0.02998 0.43306 8.88889
35 5BO9 SIA GAL NGS 0.04817 0.40212 9.17431
36 3ZZS TRP 0.01703 0.40488 9.23077
37 3MTX PGT 0.04032 0.40512 9.27152
38 2P8O BVA 0.01373 0.41235 9.27835
39 5BYZ 4WE 0.04063 0.40614 9.33333
40 4YZN 4K5 0.01579 0.41451 9.63303
41 2QZ3 XYP XYP XYP 0.02065 0.41028 10.2703
42 1KGI T4A 0.00991 0.42803 11.0236
43 2BL9 NDP 0.04428 0.40461 11.1111
44 2BL9 CP6 0.04428 0.40461 11.1111
45 4RIF 3R2 0.007792 0.44183 11.9266
46 4ZL4 4PK 0.01598 0.41918 11.9266
47 5U6C 7YS 0.02417 0.40602 12.3853
48 4NMC 2OP 0.01988 0.42743 12.844
49 5FBN 5WF 0.03129 0.41105 13.7778
50 4WZA ADP 0.02325 0.44168 15.1111
51 5DQ8 FLF 0.02906 0.40609 19.2661
52 5J75 6GQ 0.005621 0.42944 38.9908
Pocket No.: 2; Query (leader) PDB : 3KDM; Ligand: TES; Similar sites found: 21
This union binding pocket(no: 2) in the query (biounit: 3kdm.bio2) has 12 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 4WQM FAD 0.0324 0.40164 3.21101
2 4N02 FNR 0.01917 0.41389 3.55556
3 5DEP UD1 0.03141 0.41157 4.88889
4 4EHU ANP 0.01864 0.41029 5.04587
5 4IMO PWZ 0.01188 0.40004 5.11364
6 4D4U FUC GAL 0.006968 0.40794 5.33333
7 5EPO NAP 0.02893 0.40873 5.77778
8 2XVD AS6 0.02292 0.4113 5.9633
9 4P5Z Q7M 0.04123 0.40706 6.22222
10 5JFS 6K0 0.04386 0.4107 6.88073
11 2HZQ STR 0.007616 0.4005 7.47126
12 5IKB KAI 0.008191 0.4175 8.25688
13 1TLL FAD 0.02091 0.40778 8.44444
14 3RFA SAM 0.01583 0.40711 8.44444
15 2ZAT NAP 0.03723 0.40686 8.44444
16 4CNG SAH 0.0196 0.42076 10.0917
17 2WQQ CSF 0.006527 0.4317 10.6667
18 4QA8 PJZ 0.02879 0.4006 10.6667
19 4NMC FAD 0.01514 0.43051 12.844
20 2BOS GLA GAL GLC 0.004024 0.44248 19.1176
21 2BOS GLA GAL 0.004611 0.43686 19.1176
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