FAIRMol

Z64648195

Pose ID 9287 Compound 3183 Pose 479

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
T14
T. brucei ODC (G418 binding site) T. brucei G418 binding site
Ligand Z64648195
PDB1NJJ↗

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 but geometrically suspicious
Binding strong Geometry low Native mixed SASA done
Strain ΔE
16.8 kcal/mol
Protein clashes
9
Internal clashes
9
Native overlap
contact recall 0.47, Jaccard 0.37, H-bond role recall 0.00
Burial
71%
Hydrophobic fit
65%
Reason: 9 protein-contact clashes, 9 internal clashes
9 protein-contact clashes 9 intramolecular clashes 45% of hydrophobic surface appears solvent-exposed (10/22 atoms). Partial exposure is common but may limit selectivity and membrane permeability.
Molecular report
Full metrics ↗
Promising Reasonable quality metrics. Warrants further investigation.
✓ Excellent LE (-0.711 kcal/mol/HA) ✓ Good fit quality (FQ -6.92) ✓ Good H-bonds (3 bonds) ✓ Deep burial (71% SASA buried) ✓ Lipophilic contacts well-matched (65%) ✗ Moderate strain (16.8 kcal/mol) ✗ Geometry warnings ✗ Internal clashes (9)
Score
-22.026
kcal/mol
LE
-0.711
kcal/mol/HA
Fit Quality
-6.92
FQ (Leeson)
HAC
31
heavy atoms
MW
452
Da
LogP
5.10
cLogP
Final rank
4.6385
rank score
Inter norm
-0.727
normalised
Contacts
11
H-bonds 5
Strain ΔE
16.8 kcal/mol
SASA buried
71%
Lipo contact
65% BSA apolar/total
SASA unbound
699 Ų
Apolar buried
322 Ų

Interaction summary

HBA 3 HY 5 PI 0 CLASH 9

HBD/HBA · H-bonds (geometric)
HBD = ligand donates H · HBA = ligand accepts H · ~ = weak (≥110°). Mode: strict. Residues: 3.

PI · π–π interactions
No pi · π–π interactions detected for this pose.

HY · Hydrophobic contacts

CLASH · Clashes

Native ligand reference

★ reference
Interaction fingerprint calculated directly from the uploaded native ligand without docking. Current H-bond mode: strict.
Name1NJJContacts15
PoseOpen native poseHB0
IFP residues
ARG22 ARG242 ARG337 ARG342 ASP243 ASP385 GLN341 GLU384 LEU25 LEU339 LEU382 PRO340 PRO344 SER282 THR241
Current overlap7Native recall0.47
Jaccard0.37RMSD-
HB strict0Strict recall0.00
HB same residue+role0HB role recall0.00
HB same residue2HB residue recall0.40

Protein summary

398 residues
Protein targetT14Atoms6140
Residues398Chains1
Residue summaryVAL:592; LEU:513; LYS:484; ARG:432; PHE:420; ILE:418; ASP:349; THR:322; TYR:315; PRO:308; GLU:301; ALA:290; SER:253; GLY:217; ASN:210; GLN:170

Receptor context

1 kept / 0 excluded
Receptor context filtering: interactions and SASA are computed against protein atoms plus allowed cofactors/ions. Native ligand-like HETATM partners are excluded from scoring.
Kept context 1 Excluded HETATM 0
Kept cofactors / ions
A:ORX602

All stored poses for this docking hit

PoseFinal rankInter normScoreHBCTCT overlapCT recallHB role rec.RMSDExcluded
479 0.932266955788502 -0.948942 -28.7392 6 17 0 0.00 0.00 - no Open
462 2.904350206753341 -0.887834 -24.5104 10 15 0 0.00 0.00 - no Open
459 3.5339060627915737 -1.00826 -23.847 7 19 0 0.00 0.00 - no Open
464 3.5753226198764536 -0.819839 -22.2419 13 13 0 0.00 0.00 - no Open
479 4.63852025203437 -0.727277 -22.0257 5 11 7 0.47 0.00 - no Current

Molecular metrics

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

Scoring & efficiency
Docking score -22.026kcal/mol
Ligand efficiency (LE) -0.7105kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -6.922
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 31HA

Physicochemical properties
Molecular weight 451.6Da
Lipinski: ≤ 500 Da
LogP (cLogP) 5.10
Lipinski: ≤ 5
Rotatable bonds 5

Conformational strain (MMFF94s)
Strain energy (ΔE) 16.76kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy 6.76kcal/mol
Minimised FF energy -10.00kcal/mol

SASA & burial

✓ computed
SASA (unbound) 699.5Ų
Total solvent-accessible surface area of free ligand
BSA total 496.9Ų
Buried surface area upon binding
BSA apolar 322.4Ų
Hydrophobic contacts buried
BSA polar 174.5Ų
Polar contacts buried
Fraction buried 71.0%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 64.9%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -2496.9Ų
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 3349.0Ų
Non-polar SASA of receptor alone (VdW proxy, nonpolar atoms only)
Complex non-polar SASA 1368.0Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)