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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 208 families.
1 3KDM Kd = 0.1 uM TES C19 H28 O2 C[C@]12CC[....
70% Homology Family (6)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1205 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 5BJZ - MAL C12 H22 O11 C([C@@H]1[....
4 3PGF - GLC GLC n/a n/a
5 3LEV - ATP C10 H16 N5 O13 P3 c1nc(c2c(n....
6 4DVR - 0LY C17 H24 Br N3 O2 CC1(CC(CC(....
50% Homology Family (21)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1039 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 1NC2 - DOE C27 H41 N5 O10 S c1cc(ccc1C....
7 2HVK - TBA C16 H36 N CCCC[N+](C....
8 5DUB - GLY 5GG GLY ALA n/a n/a
9 5MES ic50 = 0.045 uM 7LT C44 H49 Cl2 N5 O4 CN1CCCN[C@....
10 6FS0 Kd = 0.00017 uM E4W C35 H34 Cl N5 O3 S2 Cc1c-2c(nn....
11 5BJZ - MAL C12 H22 O11 C([C@@H]1[....
12 3PGF - GLC GLC n/a n/a
13 1FE8 - NAG C8 H15 N O6 CC(=O)N[C@....
14 3LEV - ATP C10 H16 N5 O13 P3 c1nc(c2c(n....
15 1E4X Kd = 25 nM VAL VAL SER HIS PHE ASN ASP n/a n/a
16 4MA7 - P2Z C17 H20 N2 S CN(C)CCCN1....
17 4MA8 - Z80 C17 H19 Cl N2 S CN(C)CCCN1....
18 4DVR - 0LY C17 H24 Br N3 O2 CC1(CC(CC(....
19 4UUJ - XA7 C24 H52 N CCCCCC[N+]....
20 2DWE - TBA C16 H36 N CCCC[N+](C....
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 with APoc: 130
This union binding pocket(no: 1) in the query (biounit: 3kdm.bio1) has 12 residues
No: Leader PDB Ligand Sequence Similarity
1 5ISY NAD 2.22222
2 4EIL NDP 2.29358
3 4AG8 AXI 2.29358
4 4I6H 1C8 2.66667
5 3FPF MTA 2.66667
6 3FPF TNA 2.66667
7 5MYD DUP 2.66667
8 2YG2 S1P 2.90698
9 2YG2 FLC 2.90698
10 2I3G NAP 3.11111
11 1DZK PRZ 3.18471
12 3P7N FMN 3.21101
13 4YBN FAD 3.21101
14 6H45 QEI 3.21101
15 2A8Y MTA 3.21101
16 1K3A ACP 3.21101
17 3EE4 MYR 3.55556
18 1YF4 CYS TYR PHE GLN ASN CYS PRO ARG GLY NH2 3.58744
19 1YBH FAD 3.66972
20 2X24 X24 3.66972
21 5FLJ QUE 3.76344
22 4V03 ADP 4
23 2FCR FMN 4.04624
24 3GNE FLC 4.12844
25 6BFG FMN 4.12844
26 1N5D NDP 4.12844
27 4TXJ THM 4.44444
28 1QS8 IVA VAL VAL STA ALA STA 4.44444
29 2IYA UDP 4.44444
30 4H6Q TFB 4.44444
31 4H6Q FAD 4.44444
32 4L9Z OXL 4.58716
33 4L9Z COA 4.58716
34 4RFM 3P6 4.58716
35 6C3C EJ1 4.58716
36 2UV4 AMP 4.60526
37 2CM4 RCL 4.66667
38 4ORR PE3 4.73684
39 4BCM T7Z 4.88889
40 1TIW TFB 4.88889
41 1TIW FAD 4.88889
42 3KV8 FAH 5.03597
43 1UM0 FMN 5.04587
44 1IHU AF3 5.04587
45 1IHU ADP 5.04587
46 3WWC BUA 5.04587
47 1PZO CBT 5.04587
48 3NW7 LGV 5.33333
49 1PMO PLR 5.33333
50 6GBV FMN 5.47945
51 4G31 0WH 5.50459
52 1W62 PYC 5.50459
53 3FW4 CAQ 5.61798
54 2WPU KYT 5.66038
55 5TA6 79D 5.77778
56 3VEH 0GA 5.77778
57 2WKQ FMN 5.77778
58 4K49 HFQ 5.88235
59 5TO8 7FM 5.9633
60 2XIQ MLC 5.9633
61 2YBQ SAH 5.9633
62 4F9C 0SX 5.9633
63 1VBO MAN MAN MAN 6.04027
64 4WUJ FMN 6.12245
65 1AJ0 SAN 6.22222
66 1AJ0 PH2 6.22222
67 4F2Q QUS 6.22222
68 4AT3 LTI 6.42202
69 3FJO FMN 6.42202
70 4ZSI 4R1 6.43275
71 4H2D FMN 6.66667
72 4YHB FAD 6.66667
73 1WAP TRP 6.66667
74 2AEL SAZ 6.66667
75 5KY3 GFB 6.88073
76 5UIU 8CG 6.88073
77 4ZXA H8N 7.14286
78 1K97 ASP 7.33945
79 1K97 CIR 7.33945
80 2HZQ STR 7.47126
81 5W4W 9WG 7.55556
82 3DLS ADP 8
83 2QG6 NMN 8.0402
84 5LJI FMN 8.10811
85 1QAW TRP 8.10811
86 5C8L GLC 8.24176
87 1ELU CSS 8.25688
88 1TLL FMN 8.44444
89 4B7X NAP 8.44444
90 3RI1 3RH 8.44444
91 1KBJ FMN 8.44444
92 5EYK 5U5 8.47458
93 5EOB 5QQ 8.88889
94 3C1X CKK 8.88889
95 5BO9 SIA GAL NGS 9.17431
96 3ZZS TRP 9.23077
97 3MTX PGT 9.27152
98 2P8O BVA 9.27835
99 2V58 LZJ 9.33333
100 6E2O S0L 9.33333
101 4WNP 3RJ 9.33333
102 2CWH PYC 9.33333
103 4YZN 4K5 9.63303
104 5MY8 RXZ 9.77778
105 1ZHX HC3 10.2222
106 3GNI ATP 10.2222
107 2X61 CH 10.6667
108 1KGI T4A 11.0236
109 2BL9 NDP 11.1111
110 2BL9 CP6 11.1111
111 1I7Q BEZ 11.4679
112 1KOJ PAN 11.5556
113 4IDT T28 11.5556
114 4HK8 XYP XYP XYP XYP XYP XYP 11.6402
115 4RIF 3R2 11.9266
116 4ZL4 4PK 11.9266
117 5U6C 7YS 12.3853
118 4NMC 2OP 12.844
119 5OM2 DXT 13.3333
120 5GP0 GPP 13.4228
121 5FBN 5WF 13.7778
122 5LU5 M7P 14.7208
123 4WZA ADP 15.1111
124 2ZYI STE 16
125 4O4K 2PK 16.055
126 3HZT J60 17.7778
127 3T4L ZEA 18.8889
128 5DQ8 FLF 19.2661
129 5J75 6GQ 38.9908
130 4OH4 ANP 42.8571
Pocket No.: 2; Query (leader) PDB : 3KDM; Ligand: TES; Similar sites found with APoc: 74
This union binding pocket(no: 2) in the query (biounit: 3kdm.bio2) has 12 residues
No: Leader PDB Ligand Sequence Similarity
1 1XG5 NAP 2.75229
2 2Z81 PCJ 2.75229
3 1G2O IMH 3.11111
4 2Q0L FAD 3.21101
5 4WQM FAD 3.21101
6 6F5Z SAH 3.4632
7 4N02 FNR 3.55556
8 1F0X FAD 3.66972
9 1ST0 GTG 4.12844
10 1SJD NPG 4.12844
11 3STD MQ0 4.24242
12 4IAW LIZ 4.25532
13 3WDM ADN 4.58716
14 4N9I PCG 4.7619
15 5DEP UD1 4.88889
16 1X0P FAD 4.8951
17 4EHU ANP 5.04587
18 6FYZ EBE 5.04587
19 4IMO PWZ 5.11364
20 5HZ9 5M8 5.18518
21 4XU6 TDA 5.2381
22 4D4U FUC GAL 5.33333
23 4D52 GIV 5.33333
24 4D52 GXL 5.33333
25 5AOV GLV 5.50459
26 1IYK MIM 5.50459
27 5EPO NAP 5.77778
28 1Y60 H4M 5.91716
29 2XVD AS6 5.9633
30 4POW OP1 5.9633
31 1B1C FMN 6.07735
32 4P5Z Q7M 6.22222
33 3HAZ FAD 6.42202
34 5OJI NAP 6.42202
35 5OJI ISN 6.42202
36 1W4R TTP 6.66667
37 1EWF PC1 6.88073
38 5JFS 6K0 6.88073
39 4ITH RCM 6.88073
40 1EB1 ZAL PRO MMO 7.11111
41 4AX9 N5N 7.11111
42 4YMJ 4EJ 7.11111
43 3VBK COA 7.31707
44 1BVY FMN 7.33945
45 1Z0S ATP 7.55556
46 1SUW NAP 7.55556
47 3IGO ANP 7.55556
48 6CDG PRO GLY LEU TRP LYS SER 7.78443
49 5IKB KAI 8.25688
50 5UR1 YY9 8.44444
51 1TLL FAD 8.44444
52 3RFA SAM 8.44444
53 2ZAT NAP 8.44444
54 4M1U A2G MBG 8.57143
55 1YB5 NAP 9.33333
56 2HFN FMN 9.33333
57 4CNG SAH 10.0917
58 4IID NOJ 10.0917
59 2XCG XCG 10.2222
60 1RO7 CSF 10.6667
61 2WQQ CSF 10.6667
62 2X61 NGA GAL SIA 10.6667
63 4QA8 PJZ 10.6667
64 3PP0 03Q 11.4679
65 4NMC FAD 12.844
66 2RIO ADP 12.844
67 2IVD FAD 12.8889
68 2ZKJ ADP 12.8889
69 4OXX FMN 12.963
70 1HE1 GDP 14.0741
71 5U97 PIT 18.3486
72 2BOS GLA GAL GLC 19.1176
73 2BOS GLA GAL 19.1176
74 4GQP B40 35.3211
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