FAIRMol

GemmaOHDUnisi_26

Pose ID 9147 Compound 3109 Pose 339

DB SELECTIONDocking 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 GemmaOHDUnisi_26
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
17.8 kcal/mol
Protein clashes
6
Internal clashes
6
Native overlap
contact recall 0.53, Jaccard 0.33, H-bond role recall 0.20
Burial
83%
Hydrophobic fit
78%
Reason: 6 internal clashes
6 protein-contact clashes 6 intramolecular clashes
Molecular report
Full metrics ↗
Weak Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-0.428 kcal/mol/HA) ✓ Good fit quality (FQ -4.04) ✓ Good H-bonds (3 bonds) ✓ Deep burial (83% SASA buried) ✓ Lipophilic contacts well-matched (78%) ✗ Moderate strain (17.8 kcal/mol) ✗ Geometry warnings ✗ Many internal clashes (10)
Score
-11.996
kcal/mol
LE
-0.428
kcal/mol/HA
Fit Quality
-4.04
FQ (Leeson)
HAC
28
heavy atoms
MW
372
Da
LogP
5.11
cLogP
Final rank
3.8970
rank score
Inter norm
-0.849
normalised
Contacts
17
H-bonds 10
Strain ΔE
17.8 kcal/mol
SASA buried
83%
Lipo contact
78% BSA apolar/total
SASA unbound
660 Ų
Apolar buried
428 Ų

Interaction summary

HBD 2 HBA 1 HY 4 PI 0 CLASH 6

HBD/HBA · H-bonds (geometric)
HBD = ligand donates H · HBA = ligand accepts H · ~ = weak (≥110°). Mode: permissive. Residues: 2.

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: permissive.
Name1NJJContacts15
PoseOpen native poseHB0
IFP residues
ARG22 ARG242 ARG337 ARG342 ASP243 ASP385 GLN341 GLU384 LEU25 LEU339 LEU382 PRO340 PRO344 SER282 THR241
Current overlap8Native recall0.53
Jaccard0.33RMSD-
HB strict0Strict recall0.00
HB same residue+role1HB role recall0.20
HB same residue1HB residue recall0.20

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
385 1.2860520499306085 -0.813745 -15.6987 9 17 0 0.00 0.00 - no Open
319 1.9323249343972482 -1.23626 -33.0227 6 15 0 0.00 0.00 - no Open
345 2.215341088437669 -1.04016 -25.1848 7 17 0 0.00 0.00 - no Open
346 3.1777867617016966 -1.14625 -27.2467 9 16 0 0.00 0.00 - no Open
338 3.2462078515503885 -0.921637 -21.1922 4 16 0 0.00 0.00 - no Open
354 3.5510777675708924 -0.838749 -16.1268 5 15 0 0.00 0.00 - no Open
455 3.653448925064978 -0.888525 -22.8681 7 19 0 0.00 0.00 - no Open
339 3.8969988921781593 -0.848867 -11.9956 10 17 8 0.53 0.20 - 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 -11.996kcal/mol
Ligand efficiency (LE) -0.4284kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -4.044
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 28HA

Physicochemical properties
Molecular weight 372.4Da
Lipinski: ≤ 500 Da
LogP (cLogP) 5.11
Lipinski: ≤ 5
Rotatable bonds 7

Conformational strain (MMFF94s)
Strain energy (ΔE) 17.82kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy 86.10kcal/mol
Minimised FF energy 68.27kcal/mol

SASA & burial

✓ computed
SASA (unbound) 659.6Ų
Total solvent-accessible surface area of free ligand
BSA total 546.5Ų
Buried surface area upon binding
BSA apolar 428.3Ų
Hydrophobic contacts buried
BSA polar 118.2Ų
Polar contacts buried
Fraction buried 82.8%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 78.4%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -2481.3Ų
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 1381.7Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)