FAIRMol

Z19316194

Pose ID 9295 Compound 796 Pose 487

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 Z19316194
PDB1NJJ↗

3D complex viewer

Strict H-bonds Permissive H-bonds
Viewer legend
Protein receptor
Pocket residues
Cofactor context
Docked ligand
Overall assessment
Weak SASA cached
Promising but geometrically suspicious
Binding strong Geometry low Native mixed SASA done
Strain ΔE
29.5 kcal/mol
Protein clashes
6
Internal clashes
6
Native overlap
contact recall 0.47, Jaccard 0.37, H-bond role recall 0.40
Burial
78%
Hydrophobic fit
72%
Reason: 6 internal clashes
6 protein-contact clashes 6 intramolecular clashes 56% of hydrophobic surface appears solvent-exposed (10/18 atoms). Partial exposure is common but may limit selectivity and membrane permeability.
Molecular report
Full metrics ↗
Weak Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-0.910 kcal/mol/HA) ✓ Good fit quality (FQ -8.27) ✓ Good H-bonds (4 bonds) ✓ Deep burial (78% SASA buried) ✓ Lipophilic contacts well-matched (72%) ✗ High strain energy (29.5 kcal/mol) ✗ Geometry warnings ✗ Many internal clashes (10)
Score
-22.748
kcal/mol
LE
-0.910
kcal/mol/HA
Fit Quality
-8.27
FQ (Leeson)
HAC
25
heavy atoms
MW
353
Da
LogP
2.77
cLogP
Final rank
2.7562
rank score
Inter norm
-0.910
normalised
Contacts
11
H-bonds 5
Strain ΔE
29.5 kcal/mol
SASA buried
78%
Lipo contact
72% BSA apolar/total
SASA unbound
604 Ų
Apolar buried
343 Ų

Interaction summary

HBD 1 HBA 3 HY 3 PI 1 CLASH 6

HBD/HBA · H-bonds (geometric)
HBD = ligand donates H · HBA = ligand accepts H · ~ = weak (≥110°). Mode: strict. 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: 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 strict2Strict recall0.33
HB same residue+role2HB role recall0.40
HB same residue3HB residue recall0.60

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
485 0.5414038736159136 -1.02325 -26.5224 2 14 0 0.00 0.00 - no Open
480 0.5893495661711086 -1.28655 -32.866 5 11 0 0.00 0.00 - no Open
526 1.4416750172994826 -1.05505 -27.159 3 13 0 0.00 0.00 - no Open
473 2.268489696676325 -0.970509 -24.7794 3 18 0 0.00 0.00 - no Open
487 2.756175914736965 -0.909834 -22.7484 5 11 7 0.47 0.40 - no Current
515 2.8705058620403947 -0.899289 -23.4697 5 12 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 -22.748kcal/mol
Ligand efficiency (LE) -0.9099kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -8.272
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 25HA

Physicochemical properties
Molecular weight 353.4Da
Lipinski: ≤ 500 Da
LogP (cLogP) 2.77
Lipinski: ≤ 5
Rotatable bonds 5

Conformational strain (MMFF94s)
Strain energy (ΔE) 29.46kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy 9.71kcal/mol
Minimised FF energy -19.75kcal/mol

SASA & burial

✓ computed
SASA (unbound) 604.3Ų
Total solvent-accessible surface area of free ligand
BSA total 473.4Ų
Buried surface area upon binding
BSA apolar 342.6Ų
Hydrophobic contacts buried
BSA polar 130.8Ų
Polar contacts buried
Fraction buried 78.4%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 72.4%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -2408.5Ų
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 1387.8Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)