Target Binding Site Detail

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Target General Information
Ligand General Information
Drug Binding Sites of Target
References
Target General Information  Top
Target ID T38950 Target Info
Target Name Myeloid cell surface antigen CD33 (CD33)
Synonyms Siglec-3; Sialic acid-binding Ig-like lectin 3; SIGLEC3; Gp67
Target Type Successful Target
Gene Name CD33
Biochemical Class Immunoglobulin
UniProt ID
CD33_HUMAN
Ligand General Information  Top
Ligand Name 2-aminoethyl 5-{[(4-cyclohexyl-1H-1,2,3-triazol-1-yl)acetyl]amino}-3,5,9-trideoxy-9-[(4-hydroxy-3,5-dimethylbenzene-1-carbonyl)amino]-D-glycero-alpha-D-galacto-non-2-ulopyranonosyl-(2->6)-beta-D-galactopyranosyl-(1->4)-beta-D-glucopyranoside Ligand Info
Canonical SMILES CC1=CC(=CC(=C1O)C)C(=O)NCC(C(C2C(C(CC(O2)(C(=O)O)OCC3C(C(C(C(O3)OC4C(OC(C(C4O)O)OCCN)CO)O)O)O)O)NC(=O)CN5C=C(N=N5)C6CCCCC6)O)O
InChI 1S/C42H64N6O20/c1-18-10-21(11-19(2)29(18)53)38(60)44-13-24(51)30(54)37-28(45-27(52)15-48-14-22(46-47-48)20-6-4-3-5-7-20)23(50)12-42(68-37,41(61)62)64-17-26-31(55)32(56)34(58)40(66-26)67-36-25(16-49)65-39(63-9-8-43)35(59)33(36)57/h10-11,14,20,23-26,28,30-37,39-40,49-51,53-59H,3-9,12-13,15-17,43H2,1-2H3,(H,44,60)(H,45,52)(H,61,62)/t23-,24+,25+,26+,28+,30+,31-,32-,33+,34+,35+,36+,37+,39+,40-,42+/m0/s1
InChIKey DQZXNLDRAKHEEK-XCGJJDHASA-N
PubChem Compound ID 137796754
Drug Binding Sites of Target  Top
PDB ID: 7AW6      The extracellular region of CD33 with bound sialoside analogue P22
Method X-ray diffraction Resolution 1.95 Å Mutation No [1]
PDB Sequence
GFWLQVQESV
29
TVQEGLCVLV
39
PCTFFHPIPY
49
YDKNSPVHGY
59
WFREGAIISR
69

DSPVATNKLD
79
QEVQEETQGR
89
FRLLGDPSRN
99
NCSLSIVDAR
109
RRDNGSYFFR
119

MERGSTKYSY
129
KSPQLSVHVT
139
DLTHRPKILI
149
PGTLEPGHSK
159
NLTCSVSWAC
169

EQGTPPIFSW
179
LSAAPTSLGP
189
RTTHSSVLII
199
TPRPQDHGTN
209
LTCQVKFAGA
219

GVTTERTIQL
229
NVT
Residue
Distance (Å)
PHE21
3.724
PRO46
3.905
PRO48
4.247
TYR50
3.545
ILE67
4.684
SER68
3.414
PHE117
3.568
ARG119
2.634
Residue
Distance (Å)
SER124
4.685
THR125
4.504
LYS126
2.815
TYR127
3.762
SER128
2.908
TYR129
3.840
LYS130
3.541
GLN133
4.246
PDB ID: 6D4A      Cell Surface Receptor with Bound Ligand at 1.75-A Resolution
Method X-ray diffraction Resolution 1.75 Å Mutation No [2]
PDB Sequence
NFWLQVQESV
29
TVQEGLCVLV
39
PCTFFHPIPY
49
YDKNSPVHGY
59
WFREGAIISR
69

DSPVATNKLD
79
QEVQEETQGR
89
FRLLGDPSRN
99
NCSLSIVDAR
109
RRDNGSYFFR
119

MERGSTKYSY
129
KSPQLSVHVT
139
DLT
Residue
Distance (Å)
PHE21
3.398
PRO46
4.433
PRO48
4.370
TYR50
3.418
PHE117
3.537
ARG119
2.736
SER124
4.475
Residue
Distance (Å)
THR125
4.247
LYS126
2.731
TYR127
3.738
SER128
2.726
TYR129
3.835
LYS130
3.507
GLN133
3.773
PDB ID: 6D49      Cell Surface Receptor in Complex with Ligand at 1.80-A Resolution
Method X-ray diffraction Resolution 1.80 Å Mutation No [2]
PDB Sequence
GDPNFWLQVQ
26
ESVTVQEGLC
36
VLVPCTFFHP
46
IPYYDKNSPV
56
HGYWFREGAI
66

ISRDSPVATN
76
KLDQEVQEET
86
QGRFRLLGDP
96
SRNNCSLSIV
106
DARRRDNGSY
116

FFRMERGSTK
126
YSYKSPQLSV
136
HVTDLT
Residue
Distance (Å)
GLY17
4.039
ASP18
3.442
ASN20
3.292
PHE21
3.568
PRO46
4.078
PRO48
4.379
TYR50
4.220
ILE66
3.580
SER68
2.921
ARG69
4.476
Residue
Distance (Å)
PHE117
3.578
ARG119
2.768
SER124
4.644
THR125
4.238
LYS126
2.788
TYR127
3.769
SER128
2.877
TYR129
3.640
LYS130
3.333
GLN133
4.007
References  Top
REF 1 The extracellular region of CD33 with bound sialoside analogue P22
REF 2 Small Molecule Binding to Alzheimer Risk Factor CD33 Promotes Abeta Phagocytosis. iScience. 2019 Sep 27;19:110-118.

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