FAIRMol

Z19456272

Pose ID 8580 Compound 100 Pose 450

DB fairmolDocking pose analysis is being read from this database.
Compound detail Protein structures Back to compounds
Molecular metrics status: done
RDKit SASA-based burial metrics are cached.
SASA cached
T13
T. brucei ODC (Active site) T. brucei Active site
Ligand Z19456272
PDB1F3T↗

3D complex viewer

Strict H-bonds Permissive H-bonds
Viewer legend
Protein receptor
Pocket residues
Cofactor context
Docked ligand
Overall assessment
Promising SASA cached
Promising and worth follow-up
Binding strong Geometry medium Native strong SASA done
Strain ΔE
17.9 kcal/mol
Protein clashes
3
Internal clashes
3
Native overlap
contact recall 0.74, Jaccard 0.58, H-bond role recall 0.43
Burial
82%
Hydrophobic fit
66%
Reason: no major geometry red flags detected
3 protein-contact clashes 3 intramolecular clashes
Molecular report
Full metrics ↗
Promising Reasonable quality metrics. Warrants further investigation.
✓ Excellent LE (-0.905 kcal/mol/HA) ✓ Good fit quality (FQ -8.82) ✓ Strong H-bond network (7 bonds) ✓ Deep burial (82% SASA buried) ✓ Lipophilic contacts well-matched (66%) ✗ Moderate strain (17.9 kcal/mol) ✗ Geometry warnings ✗ Internal clashes (9)
Score
-28.054
kcal/mol
LE
-0.905
kcal/mol/HA
Fit Quality
-8.82
FQ (Leeson)
HAC
31
heavy atoms
MW
462
Da
LogP
2.78
cLogP
Final rank
3.4356
rank score
Inter norm
-1.008
normalised
Contacts
19
H-bonds 9
Strain ΔE
17.9 kcal/mol
SASA buried
82%
Lipo contact
66% BSA apolar/total
SASA unbound
650 Ų
Apolar buried
347 Ų

Interaction summary

HBA 7 HY 4 PI 3 CLASH 3

HBD/HBA · H-bonds (geometric)
HBD = ligand donates H · HBA = ligand accepts H · ~ = weak (≥110°). Mode: permissive. Residues: 4.

PI · π–π interactions
Native π–π recall is disabled because no explicit native π–π reference was stored.

HY · Hydrophobic contacts

CLASH · Clashes

Native ligand reference

★ reference
Interaction fingerprint calculated directly from the uploaded native ligand without docking. Current H-bond mode: permissive.
Name1F3TContacts19
PoseOpen native poseHB0
IFP residues
ALA111 ALA67 ARG154 ARG277 ASP332 ASP88 CYS70 GLU274 GLY236 GLY237 GLY276 HIS197 LYS69 PHE238 PRO275 SER200 TYR278 TYR331 TYR389
Current overlap14Native recall0.74
Jaccard0.58RMSD-
HB strict4Strict recall0.44
HB same residue+role3HB role recall0.43
HB same residue3HB residue recall0.43

Protein summary

411 residues
Protein targetT13Atoms6340
Residues411Chains1
Residue summaryVAL:624; LEU:551; LYS:506; ARG:480; PHE:460; ILE:418; ASP:348; GLU:332; THR:322; TYR:315; PRO:308; ALA:290; SER:264; GLY:224; ASN:210; GLN:170

All stored poses for this docking hit

PoseFinal rankInter normScoreHBCTCT overlapCT recallHB role rec.RMSDExcluded
458 0.27097943228209714 -0.811185 -19.6635 2 14 0 0.00 0.00 - no Open
513 0.9544730494110983 -0.848599 -22.718 5 16 0 0.00 0.00 - no Open
139 1.2196504051403532 -0.732121 -21.3242 5 16 1 0.05 0.00 - no Open
506 1.3741049807450607 -0.848148 -20.44 3 19 0 0.00 0.00 - no Open
114 1.8007768117229013 -0.767307 -20.1444 8 15 0 0.00 0.00 - no Open
131 1.8058017168282356 -0.940039 -24.6674 6 14 0 0.00 0.00 - no Open
117 2.0182178879377184 -0.829303 -24.0955 5 14 0 0.00 0.00 - no Open
485 2.0994881049338083 -0.856427 -22.7639 4 13 0 0.00 0.00 - no Open
105 2.2832214801183897 -0.874039 -22.0808 4 17 0 0.00 0.00 - no Open
453 2.83121549954444 -0.908661 -22.7336 12 15 0 0.00 0.00 - no Open
447 2.8591163001678837 -0.882026 -22.5359 9 16 0 0.00 0.00 - no Open
525 2.939096492500812 -0.773608 -21.4384 5 12 0 0.00 0.00 - no Open
64 2.9866007130431282 -0.949521 -25.285 13 16 0 0.00 0.00 - no Open
450 3.435617077931159 -1.00835 -28.0542 9 19 14 0.74 0.43 - no Current
91 3.5725886357035477 -0.950541 -26.1853 11 15 0 0.00 0.00 - no Open
89 3.588860201862459 -0.897555 -24.8412 10 10 0 0.00 0.00 - no Open
425 4.484716716621432 -0.989791 -28.8598 6 13 0 0.00 0.00 - no Open

Molecular metrics

RDKit SASA burial, strain energy (MMFF94s), ligand efficiency and fit quality for this docking pose.
✓ Metrics available

Scoring & efficiency
Docking score -28.054kcal/mol
Ligand efficiency (LE) -0.9050kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -8.817
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 31HA

Physicochemical properties
Molecular weight 461.5Da
Lipinski: ≤ 500 Da
LogP (cLogP) 2.78
Lipinski: ≤ 5
Rotatable bonds 6

Conformational strain (MMFF94s)
Strain energy (ΔE) 17.95kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy 24.29kcal/mol
Minimised FF energy 6.34kcal/mol

SASA & burial

✓ computed
SASA (unbound) 650.1Ų
Total solvent-accessible surface area of free ligand
BSA total 529.8Ų
Buried surface area upon binding
BSA apolar 347.1Ų
Hydrophobic contacts buried
BSA polar 182.7Ų
Polar contacts buried
Fraction buried 81.5%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 65.5%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -2518.0Ų
SASA_nonpolar(complex) − SASA_nonpolar(receptor) − SASA_nonpolar(ligand free). Negative = non-polar surface buried upon binding. Requires full polarity-decomposed SASA computation.
Receptor non-polar SASA 3461.2Ų
Non-polar SASA of receptor alone (VdW proxy, nonpolar atoms only)
Complex non-polar SASA 1375.5Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)