Receptor
PDB id Resolution Class Description Source Keywords
2GJ5 2.4 Å NON-ENZYME: TRANSPORT CRYSTAL STRUCTURE OF A SECONDARY VITAMIN D3 BINDING SITE OF MILK BETA-LACTOGLOBULIN BOS TAURUS BETA-LACTOGLOBULIN VITAMIN D3 TRANSPORT PROTEIN
Ref.: CRYSTAL STRUCTURE OF A SECONDARY VITAMIN D3 BINDING SITE OF MILK BETA-LACTOGLOBULIN. PROTEINS V. 71 1197 2008
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
VD3 A:163;
A:164;
Valid;
Valid;
none;
none;
Kd = 4.74 nM
384.638 C27 H44 O CC(C)...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
2GJ5 2.4 Å NON-ENZYME: TRANSPORT CRYSTAL STRUCTURE OF A SECONDARY VITAMIN D3 BINDING SITE OF MILK BETA-LACTOGLOBULIN BOS TAURUS BETA-LACTOGLOBULIN VITAMIN D3 TRANSPORT PROTEIN
Ref.: CRYSTAL STRUCTURE OF A SECONDARY VITAMIN D3 BINDING SITE OF MILK BETA-LACTOGLOBULIN. PROTEINS V. 71 1197 2008
Members (19)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 199 families.
1 3NQ3 Kd = 166 uM DKA C10 H20 O2 CCCCCCCCCC....
2 1GX8 - RTL C20 H30 O CC1=C(C(CC....
3 3UEX - STE C18 H36 O2 CCCCCCCCCC....
4 1B0O - PLM C16 H32 O2 CCCCCCCCCC....
5 3UEV Ka = 778000 M^-1 MYR C14 H28 O2 CCCCCCCCCC....
6 1GX9 - REA C20 H28 O2 CC1=C(C(CC....
7 3UEW Ka = 2040000 M^-1 PLM C16 H32 O2 CCCCCCCCCC....
8 3NQ9 Kd = 92.6 uM OCA C8 H16 O2 CCCCCCCC(=....
9 3UEU Ka = 172000 M^-1 DAO C12 H24 O2 CCCCCCCCCC....
10 4IB6 Ka = 248000 M^-1 DAO C12 H24 O2 CCCCCCCCCC....
11 4Y0Q Ka = 3000 M^-1 PX9 C17 H27 N O3 CCCCOc1ccc....
12 2GJ5 Kd = 4.74 nM VD3 C27 H44 O CC(C)CCC[C....
13 4Y0P Ka = 885 M^-1 TE4 C15 H24 N2 O2 CCCCNc1ccc....
14 1BSO - BRC C12 H23 Br O2 C(CCCCCC(=....
15 4Y0R Ka = 3000 M^-1 PX9 C17 H27 N O3 CCCCOc1ccc....
16 5K06 - MYR C14 H28 O2 CCCCCCCCCC....
17 5HTD - MYR C14 H28 O2 CCCCCCCCCC....
18 1GXA - PLM C16 H32 O2 CCCCCCCCCC....
19 4Y0S Ka = 20800 M^-1 PX9 C17 H27 N O3 CCCCOc1ccc....
70% Homology Family (19)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 166 families.
1 3NQ3 Kd = 166 uM DKA C10 H20 O2 CCCCCCCCCC....
2 1GX8 - RTL C20 H30 O CC1=C(C(CC....
3 3UEX - STE C18 H36 O2 CCCCCCCCCC....
4 1B0O - PLM C16 H32 O2 CCCCCCCCCC....
5 3UEV Ka = 778000 M^-1 MYR C14 H28 O2 CCCCCCCCCC....
6 1GX9 - REA C20 H28 O2 CC1=C(C(CC....
7 3UEW Ka = 2040000 M^-1 PLM C16 H32 O2 CCCCCCCCCC....
8 3NQ9 Kd = 92.6 uM OCA C8 H16 O2 CCCCCCCC(=....
9 3UEU Ka = 172000 M^-1 DAO C12 H24 O2 CCCCCCCCCC....
10 4IB6 Ka = 248000 M^-1 DAO C12 H24 O2 CCCCCCCCCC....
11 4Y0Q Ka = 3000 M^-1 PX9 C17 H27 N O3 CCCCOc1ccc....
12 2GJ5 Kd = 4.74 nM VD3 C27 H44 O CC(C)CCC[C....
13 4Y0P Ka = 885 M^-1 TE4 C15 H24 N2 O2 CCCCNc1ccc....
14 1BSO - BRC C12 H23 Br O2 C(CCCCCC(=....
15 4Y0R Ka = 3000 M^-1 PX9 C17 H27 N O3 CCCCOc1ccc....
16 5K06 - MYR C14 H28 O2 CCCCCCCCCC....
17 5HTD - MYR C14 H28 O2 CCCCCCCCCC....
18 1GXA - PLM C16 H32 O2 CCCCCCCCCC....
19 4Y0S Ka = 20800 M^-1 PX9 C17 H27 N O3 CCCCOc1ccc....
50% Homology Family (19)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 141 families.
1 3NQ3 Kd = 166 uM DKA C10 H20 O2 CCCCCCCCCC....
2 1GX8 - RTL C20 H30 O CC1=C(C(CC....
3 3UEX - STE C18 H36 O2 CCCCCCCCCC....
4 1B0O - PLM C16 H32 O2 CCCCCCCCCC....
5 3UEV Ka = 778000 M^-1 MYR C14 H28 O2 CCCCCCCCCC....
6 1GX9 - REA C20 H28 O2 CC1=C(C(CC....
7 3UEW Ka = 2040000 M^-1 PLM C16 H32 O2 CCCCCCCCCC....
8 3NQ9 Kd = 92.6 uM OCA C8 H16 O2 CCCCCCCC(=....
9 3UEU Ka = 172000 M^-1 DAO C12 H24 O2 CCCCCCCCCC....
10 4IB6 Ka = 248000 M^-1 DAO C12 H24 O2 CCCCCCCCCC....
11 4Y0Q Ka = 3000 M^-1 PX9 C17 H27 N O3 CCCCOc1ccc....
12 2GJ5 Kd = 4.74 nM VD3 C27 H44 O CC(C)CCC[C....
13 4Y0P Ka = 885 M^-1 TE4 C15 H24 N2 O2 CCCCNc1ccc....
14 1BSO - BRC C12 H23 Br O2 C(CCCCCC(=....
15 4Y0R Ka = 3000 M^-1 PX9 C17 H27 N O3 CCCCOc1ccc....
16 5K06 - MYR C14 H28 O2 CCCCCCCCCC....
17 5HTD - MYR C14 H28 O2 CCCCCCCCCC....
18 1GXA - PLM C16 H32 O2 CCCCCCCCCC....
19 4Y0S Ka = 20800 M^-1 PX9 C17 H27 N O3 CCCCOc1ccc....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: VD3; Similar ligands found: 24
No: Ligand ECFP6 Tc MDL keys Tc
1 VD3 1 1
2 VDY 0.78481 0.921053
3 YS2 0.556818 0.772727
4 VDX 0.553191 0.853659
5 YSV 0.532609 0.853659
6 VDZ 0.532609 0.853659
7 MVD 0.525773 0.853659
8 VD2 0.516129 0.829268
9 C33 0.514852 0.833333
10 O1C 0.509804 0.795455
11 ZNE 0.504673 0.641509
12 YS3 0.5 0.829268
13 C3O 0.490385 0.76087
14 VD1 0.488636 0.804878
15 YSD 0.484211 0.785714
16 OCC 0.481132 0.744681
17 TEJ 0.470588 0.717391
18 TX5 0.46 0.809524
19 AKX 0.457944 0.790698
20 BIV 0.435644 0.853659
21 JC1 0.423077 0.755556
22 7ZU 0.401961 0.804878
23 MC9 0.401961 0.761905
24 ICJ 0.4 0.833333
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 2GJ5; Ligand: VD3; Similar sites found: 222
This union binding pocket(no: 1) in the query (biounit: 2gj5.bio1) has 37 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 2OVD DAO 0.0001315 0.5472 None
2 2GUE NAG 0.001632 0.50095 None
3 4MA6 28E 0.001324 0.49064 None
4 4GGZ BTN 0.002437 0.4657 None
5 5D3X 4IP 0.006468 0.46197 None
6 5DG2 GAL GLC 0.001003 0.45773 None
7 5OO5 UUA 0.0024 0.45235 None
8 2NU5 NAG 0.01019 0.44644 None
9 3BRN SRO 0.01295 0.43775 None
10 2BYC FMN 0.007027 0.43771 None
11 1DZT TPE 0.01459 0.43324 None
12 4RHS SIA SIA GAL 0.02393 0.43316 None
13 4WUJ FMN 0.005248 0.42865 None
14 1QIN GIP 0.001004 0.42523 None
15 2Z6C FMN 0.006549 0.4242 None
16 4MNS 2AX 0.001193 0.42061 None
17 1N5S ADL 0.01139 0.41971 None
18 3T50 FMN 0.009487 0.41674 None
19 2BOS GLA GAL GLC 0.02057 0.41159 None
20 1H4H XYP XYS XYP 0.01676 0.41159 None
21 2BOS GLA GAL 0.02005 0.40908 None
22 5HA0 LTD 0.001107 0.43824 1.28205
23 3EW2 BTN 0.002509 0.46505 1.48148
24 1OGX EQU 0.01839 0.41301 2.29008
25 3FW3 ETS 0.01942 0.41915 2.46914
26 4RLT FSE 0.009086 0.43207 2.53165
27 4EES FMN 0.0102 0.41214 2.6087
28 5FPX GLY SER SER HIS HIS HIS HIS HIS 0.002972 0.44008 2.65487
29 4Z28 BTN 0.002443 0.46564 2.98507
30 2HKA C3S 0.003436 0.43717 3.07692
31 3PUR 2HG 0.02184 0.42655 3.08642
32 4GCZ FMN 0.006666 0.42385 3.08642
33 4JGP PYR 0.02457 0.42375 3.08642
34 2WKQ FMN 0.01025 0.41519 3.08642
35 1ZDT PEF 0.004857 0.41168 3.08642
36 4H69 10Y 0.03086 0.40867 3.08642
37 3N9O OGA 0.04668 0.40538 3.08642
38 5BYZ 4WE 0.005102 0.40067 3.08642
39 4XBT FLC 0.01007 0.41883 3.22581
40 5FQK 6NT 0.02489 0.4218 3.34572
41 2V0U FMN 0.01017 0.41533 3.42466
42 5EFW FMN 0.01335 0.40986 3.44828
43 5DJU FMN 0.01604 0.40318 3.44828
44 3VY6 BGC BGC 0.01308 0.43406 3.5461
45 5SVV FMN 0.01332 0.40686 3.64964
46 4AZT LY2 0.003339 0.45865 3.7037
47 4ZNO SUC 0.01037 0.45134 3.7037
48 2VFT SOR 0.005005 0.44959 3.7037
49 1J3R 6PG 0.005833 0.44616 3.7037
50 1SDW IYT 0.01476 0.42142 3.7037
51 3FW9 SLX 0.0131 0.41023 3.7037
52 2VGD XYP XYP 0.02716 0.40549 3.7037
53 3FHR P4O 0.01835 0.40343 3.7037
54 4UTW RFW 0.03179 0.40118 3.7037
55 5H9Q TD2 0.0008764 0.47033 3.87097
56 1WBI BTN 0.004388 0.44375 3.87597
57 3PNA CMP 0.04438 0.40394 3.8961
58 4BJ8 BTN 0.004366 0.43982 3.96825
59 5V3D FCN 0.0235 0.42138 4.13793
60 2E56 MYR 0.001145 0.42579 4.16667
61 2NLR BGC BGC G2F SHG 0.01096 0.42414 4.32099
62 2OVW CBI 0.0255 0.42096 4.32099
63 4DOL PLM 0.01719 0.40782 4.32099
64 3H7J PPY 0.02776 0.40412 4.32099
65 3JZ0 CLY 0.04954 0.40193 4.32099
66 5FXD H7Y 0.02848 0.40039 4.32099
67 4WN5 MVC 0.002866 0.43038 4.34783
68 1NKI PPF 0.04394 0.40797 4.44444
69 3I7V ATP 0.02727 0.40651 4.47761
70 5T7I LAT NAG GAL 0.009367 0.44523 4.51613
71 2PR5 FMN 0.006544 0.42422 4.54545
72 2XEM SSV 0.03777 0.40407 4.66667
73 4CPH LH4 0.01043 0.42519 4.72441
74 4K55 H6P 0.007124 0.44826 4.83871
75 2JIG PD2 0.0005701 0.50409 4.93827
76 3RGA LSB 0.001347 0.46443 4.93827
77 1H8S AIC 0.008134 0.44319 4.93827
78 3PUA OGA 0.01635 0.43414 4.93827
79 1QFT HSM 0.007586 0.42825 4.93827
80 5A86 D7E 0.0231 0.41913 4.93827
81 3SLS 77D 0.01329 0.41312 4.93827
82 4NM5 ADP 0.007272 0.4127 4.93827
83 4Z1D PEP 0.04507 0.40746 4.93827
84 1OJJ GLC GAL 0.04052 0.40607 4.93827
85 2IF8 ADP 0.04891 0.4054 4.93827
86 5F2T PLM 0.01705 0.40197 4.93827
87 4JH6 FCN 0.007935 0.44376 5.07246
88 3GGF GVD 0.006089 0.44085 5.55556
89 5L6G XYP 0.01307 0.43807 5.55556
90 4W9N TCL 0.01905 0.43008 5.55556
91 1OIJ AKG 0.01953 0.42186 5.55556
92 4ZSI GLP 0.01082 0.42079 5.55556
93 4OPC PGT 0.008816 0.41698 5.55556
94 3P7N FMN 0.01009 0.41551 5.55556
95 3HQP OXL 0.02063 0.41164 5.55556
96 4ZSI 4R1 0.01775 0.41038 5.55556
97 3E2M E2M 0.006151 0.41014 5.55556
98 1LOP SIN ALA PRO ALA NIT 0.04625 0.40891 5.55556
99 2I6A 5I5 0.01451 0.40817 5.55556
100 4QAC KK3 0.01235 0.40264 5.55556
101 1DMY AZM 0.04779 0.40221 5.55556
102 4QJP V1F 0.009526 0.40212 5.55556
103 3VV1 GAL FUC 0.002493 0.4673 5.625
104 5N17 8FK 0.04983 0.40606 5.7971
105 4XT2 43L 0.005691 0.41736 5.98291
106 4WOE ADP 0.02119 0.4266 6.17284
107 4P7X YCP 0.007004 0.4263 6.17284
108 4P7X AKG 0.007004 0.4263 6.17284
109 1O68 KIV 0.03041 0.41677 6.17284
110 3JU6 ANP 0.03866 0.41104 6.17284
111 1U0A BGC BGC BGC BGC 0.0184 0.40962 6.17284
112 4FFG LBS 0.02373 0.4049 6.17284
113 3W68 VIV 0.01275 0.40202 6.17284
114 3B00 16A 0.04271 0.40127 6.17284
115 4CQE CQE 0.01541 0.40113 6.17284
116 4OIT MAN 0.01029 0.42261 6.19469
117 3A6T 8OG 0.008044 0.42702 6.20155
118 2D6M LBT 0.004577 0.43908 6.28931
119 2CM4 RCL 0.003046 0.43253 6.66667
120 3WV6 GAL BGC 0.001418 0.47886 6.79012
121 1Z03 OCH 0.006313 0.45394 6.79012
122 1Y7P RIP 0.01639 0.4276 6.79012
123 5LUN OGA 0.02089 0.42569 6.79012
124 4DFB KAN 0.03226 0.41536 6.79012
125 3WV6 GAL GLC 0.006998 0.41511 6.79012
126 5C5T AKG 0.03348 0.41052 6.79012
127 4ITH RCM 0.009607 0.4103 6.79012
128 4DFU KAN 0.04534 0.40344 6.79012
129 4XDA RIB 0.03899 0.40335 6.79012
130 3JQ3 ADP 0.04367 0.40076 6.79012
131 1YFS ALA 0.04578 0.40046 6.79012
132 2YMZ LAT 0.001991 0.43504 6.92308
133 4JNJ BTN 0.005441 0.43915 6.95652
134 2HRL SIA GAL SIA BGC NGA CEQ 0.04678 0.40271 7.08661
135 4YVN EBS 0.003978 0.46768 7.40741
136 4OCT AKG 0.003285 0.45901 7.40741
137 5NBW 8SK 0.01109 0.42771 7.40741
138 3W21 AKG 0.01861 0.42554 7.40741
139 3K3K A8S 0.007863 0.41728 7.40741
140 4OCX MT1 0.02169 0.41665 7.40741
141 5LPZ ADP 0.01335 0.41304 7.40741
142 2DDQ HRB 0.0308 0.40871 7.40741
143 1SR9 KIV 0.04757 0.40622 7.40741
144 5BU3 4W9 0.0135 0.4037 7.40741
145 5HZ9 5M8 0.02136 0.40333 7.40741
146 3PQB VGP 0.01582 0.40062 7.40741
147 2ZHL NAG GAL GAL NAG 0.01067 0.42855 7.43243
148 5BVB DOG 0.01032 0.42179 7.57576
149 4Y24 TD2 0.003654 0.45663 7.79221
150 4GQP B40 0.02604 0.41771 8.02469
151 4HY1 19X 0.02954 0.41343 8.02469
152 5C3R AKG 0.01477 0.41095 8.02469
153 5C3R HMU 0.01477 0.41095 8.02469
154 3GC0 AMP 0.024 0.41071 8.02469
155 2Z5Y HRM 0.03585 0.40893 8.02469
156 4AU8 Z3R 0.03102 0.40855 8.02469
157 4D4U FUC NDG GAL FUC 0.001865 0.48147 8.64198
158 4D52 GIV 0.006667 0.44345 8.64198
159 4D52 GXL 0.01397 0.42923 8.64198
160 4D4U FUC 0.01289 0.42583 8.64198
161 4D4U FUC GAL NAG 0.04696 0.40669 8.64198
162 3OYW TDG 0.00636 0.45377 8.95522
163 1A78 TDG 0.01126 0.42265 8.95522
164 1W6P NDG GAL 0.02893 0.40397 8.95522
165 3T4L ZEA 0.006222 0.42873 9.25926
166 2A1L PCW 0.0006691 0.42571 9.25926
167 4J25 OGA 0.03427 0.40997 9.25926
168 3QP8 HL0 0.01878 0.40919 9.25926
169 5NVX 4YY 0.006493 0.43944 9.27835
170 4W9H 3JF 0.00751 0.43625 9.27835
171 4BKS X6C 0.04741 0.405 9.27835
172 4WVW SLT 0.02293 0.41567 9.72222
173 4XCB AKG 0.0002177 0.533 9.87654
174 4DSU BZI 0.02346 0.42564 9.87654
175 5KR7 6X9 0.01903 0.41583 9.87654
176 4QXB OGA 0.03104 0.41228 9.87654
177 5W0N UPU 0.03199 0.40105 9.87654
178 4X5S AZM 0.00397 0.46561 10.4938
179 2HZQ STR 0.01137 0.44043 10.4938
180 4ZU4 4TG 0.001919 0.45703 10.8108
181 4M26 AKG 0.03174 0.41658 11.1111
182 3ZGJ RMN 0.03842 0.41119 11.1111
183 5E89 TD2 0.02083 0.40701 11.5108
184 1TT8 PHB 0.008131 0.40241 11.7284
185 4EE7 PIS 0.01355 0.40681 12.3457
186 3PP0 03Q 0.01294 0.40174 12.3457
187 5DKK FMN 0.007529 0.4214 12.4138
188 1CKM GTP 0.01948 0.42307 12.963
189 3SHR CMP 0.03076 0.40874 12.963
190 4H3P ANP 0.02202 0.4027 12.963
191 4TYO 39X 0.03018 0.40231 13.0081
192 4L77 CNL 0.03366 0.41435 13.5802
193 1QPR PPC 0.008127 0.41354 14.1975
194 1JNQ EGT 0.01715 0.40787 14.1975
195 5AIG VPR 0.02408 0.41429 14.4
196 4MVK ACE VAL PHE PHE ALA GLU ASP NH2 0.002773 0.42472 14.8148
197 3NMV PYV 0.02095 0.40688 14.8148
198 5KEW 6SB 0.009012 0.44687 14.8936
199 4H6B 10Y 0.007005 0.44662 15.4321
200 4IAW LIZ 0.006237 0.44466 15.4321
201 4H6B 10X 0.007851 0.444 15.4321
202 3T0W DIW 0.03599 0.40381 15.4472
203 3ZO7 K6H 0.03243 0.41126 15.9574
204 5FU3 BGC BGC BGC 0.0102 0.44426 16.0377
205 4CFU 2WC 0.006825 0.4343 16.6667
206 2XMY CDK 0.003441 0.41398 16.6667
207 4BCM T7Z 0.04378 0.40806 16.6667
208 4KU7 PCG 0.03042 0.40546 16.9935
209 4RW3 IPD 0.04708 0.40256 18.5185
210 4RYV ZEA 0.02008 0.41839 18.7097
211 2GVJ DGB 0.0121 0.40877 19.1358
212 5J3Z 6FQ 0.03092 0.41601 22.2222
213 4O9S 2RY 0.004882 0.41159 26.5432
214 1BHX ASP PHE GLU GLU ILE 0.006144 0.445 26.6667
215 2YG2 S1P 0.00004564 0.41494 32.0988
216 2YG2 FLC 0.0001505 0.40988 32.0988
217 4ORR PE3 0.001527 0.43247 32.716
218 1EPB REA 0.00001576 0.55739 35.8025
219 1GT4 UNA 0.0001329 0.51284 35.8491
220 1DZK PRZ 0.000005356 0.57993 39.4904
221 3KFF ZBT 0.00001913 0.59006 41.358
222 3KFF XBT 0.00001913 0.59006 41.358
Pocket No.: 2; Query (leader) PDB : 2GJ5; Ligand: VD3; Similar sites found: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 2) in the query (biounit: 2gj5.bio1) has 9 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
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