Structure of PDB 3iu2 Chain B Binding Site BS01

Receptor Information

>3iu2 Chain B (length=379) Species: 9606 (Homo sapiens)

RSYQFWDTQPVPKLGEVVNTHGPVEPDKDNIRQEPYTLPQGFTWDALDLG
DRGVLKELYTLLNENYVEDDDNMFRFDYSPEFLLWALRPPGWLPQWHCGV
RVVSSRKLVGFISAIPANIHIYDTEKKMVEINFLCVHKKLRSKRVAPVLI
REITRRVHLEGIFQAVYTAGVVLPKPVGTCRYWHRSLNPRKLIEVKFSHL
SRNMTMQRTMKLYRLPETPKTAGLRPMETKDIPVVHQLLTRYLKQFHLTP
VMSQEEVEHWFYPQENIIDTFVVENANGEVTDFLSFYTLPSTIMNHKSLK
AAYSFYNVHTQTPLLDLMSDALVLAKMKGFDVFNALDLMENKTFLEKLKF
GIGDGNLQYYLYNWKCPSMGAEKVGLVLQ

Ligand information

• Ligand ID: MYA
• InChI: InChI=1S/C35H62N7O17P3S/c1-4-5-6-7-8-9-10-11-12-13-14-15-26(44)63-19-18-37-25(43)16-17-38-33(47)30(46)35(2,3)21-56-62(53,54)59-61(51,52)55-20-24-29(58-60(48,49)50)28(45)34(57-24)42-23-41-27-31(36)39-22-40-32(27)42/h22-24,28-30,34,45-46H,4-21H2,1-3H3,(H,37,43)(H,38,47)(H,51,52)(H,53,54)(H2,36,39,40)(H2,48,49,50)/t24-,28-,29-,30+,34-/m1/s1
• InChIKey: DUAFKXOFBZQTQE-QSGBVPJFSA-N
• SMILES:
  OpenEye OEToolkits 2.0.7: CCCCCCCCCCCCCC(=O)SCCNC(=O)CCNC(=O)C(C(C)(C)COP(=O)(O)OP(=O)(O)OCC1C(C(C(O1)n2cnc3c2ncnc3N)O)OP(=O)(O)O)O
  ACDLabs 12.01: O=C(SCCNC(=O)CCNC(=O)C(O)C(C)(C)COP(=O)(O)OP(=O)(O)OCC3OC(n2cnc1c(ncnc12)N)C(O)C3OP(=O)(O)O)CCCCCCCCCCCCC
  CACTVS 3.385: CCCCCCCCCCCCCC(=O)SCCNC(=O)CCNC(=O)[CH](O)C(C)(C)CO[P](O)(=O)O[P](O)(=O)OC[CH]1O[CH]([CH](O)[CH]1O[P](O)(O)=O)n2cnc3c(N)ncnc23
  OpenEye OEToolkits 2.0.7: CCCCCCCCCCCCCC(=O)SCCNC(=O)CCNC(=O)[C@@H](C(C)(C)COP(=O)(O)OP(=O)(O)OC[C@@H]1[C@H]([C@H]([C@@H](O1)n2cnc3c2ncnc3N)O)OP(=O)(O)O)O
  CACTVS 3.385: CCCCCCCCCCCCCC(=O)SCCNC(=O)CCNC(=O)[C@H](O)C(C)(C)CO[P](O)(=O)O[P](O)(=O)OC[C@H]1O[C@H]([C@H](O)[C@@H]1O[P](O)(O)=O)n2cnc3c(N)ncnc23
• Formula: C35 H62 N7 O17 P3 S
• Name: TETRADECANOYL-COA;
  MYRISTOYL-COA
• DrugBank: DB02180
• ZINC: ZINC000195445287
• PDB chain: 3iu2 Chain B Residue 2001

Receptor-Ligand Complex Structure

Structure summary

• PDB: 3iu2 Crystal Structure of human type-I N-myristoyltransferase with bound myristoyl-CoA and inhibitor DDD90096
• Resolution: 1.73 Å
• Binding residue (original residue number in PDB): Y117 Q118 F119 W120 Y180 V181 I245 N246 L248 V250 R255 S256 R258 A260 T268 V271 A279 Y281 T282 L287 Y479
• Binding residue (residue number reindexed from 1): Y3 Q4 F5 W6 Y66 V67 I131 N132 L134 V136 R141 S142 R144 A146 T154 V157 A165 Y167 T168 L173 Y362
• Annotation score: 3

Enzymatic activity

• Catalytic site (original residue number in PDB): N246 F247 L248 T282 Q496
• Catalytic site (residue number reindexed from 1): N132 F133 L134 T168 Q379
• Enzyme Commision number: 2.3.1.-
  2.3.1.97: glycylpeptide N-tetradecanoyltransferase.

Gene Ontology

Molecular Function

• GO:0004379 glycylpeptide N-tetradecanoyltransferase activity

Biological Process

• GO:0006499 N-terminal protein myristoylation

External links

• PDB: RCSB:3iu2, PDBe:3iu2, PDBj:3iu2
• PDBsum: 3iu2
• UniProt: P30419|NMT1_HUMAN Glycylpeptide N-tetradecanoyltransferase 1 (Gene Name=NMT1)