FAIRMol

Z56772918

Pose ID 9212 Compound 3661 Pose 404

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 Z56772918
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
Weak or marginal quality
Binding strong Geometry high Native strong SASA done
Strain ΔE
16.3 kcal/mol
Protein clashes
1
Internal clashes
1
Native overlap
contact recall 0.60, Jaccard 0.41, H-bond role recall 0.40
Burial
78%
Hydrophobic fit
74%
Reason: no major geometry red flags detected
1 protein-contact clashes
Molecular report
Full metrics ↗
Weak Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-0.706 kcal/mol/HA) ✓ Good fit quality (FQ -6.67) ✓ Good H-bonds (5 bonds) ✓ Deep burial (78% SASA buried) ✓ Lipophilic contacts well-matched (74%) ✗ Moderate strain (16.3 kcal/mol) ✗ Geometry warnings ✗ Minor protein-contact clashes (3) ✗ Many internal clashes (10)
Score
-19.773
kcal/mol
LE
-0.706
kcal/mol/HA
Fit Quality
-6.67
FQ (Leeson)
HAC
28
heavy atoms
MW
450
Da
LogP
5.67
cLogP
Strain ΔE
16.3 kcal/mol
SASA buried
78%
Lipo contact
74% BSA apolar/total
SASA unbound
676 Ų
Apolar buried
393 Ų

Interaction summary

HB 5 HY 15 PI 0 CLASH 1

HB · H-bonds
Mode: strict. Count shows atom-level H-bonds; unique residues in summary: 0.

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

HY · Hydrophobic contacts

CLASH · Clashes
Final rank0.821Score-19.773
Inter norm-0.836Intra norm0.130
Top1000noExcludedno
Contacts16H-bonds5
Artifact reasongeometry warning; 10 clashes; 3 protein contact clashes
Residues
ARG22 ARG342 ARG50 ASN20 ASP44 CYS26 GLN341 GLU343 GLU384 LEU25 LEU339 LEU382 PRO340 PRO344 THR21 THR285

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 overlap9Native recall0.60
Jaccard0.41RMSD-
HB strict2Strict recall0.33
HB same residue+role2HB role recall0.40
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
404 0.8207185216231806 -0.836326 -19.773 5 16 9 0.60 0.40 - no Current
358 1.789900415573445 -1.14473 -29.4393 4 17 0 0.00 0.00 - no Open
384 1.8277656698694202 -0.884001 -22.3379 3 16 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 -19.773kcal/mol
Ligand efficiency (LE) -0.7062kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -6.667
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 28HA

Physicochemical properties
Molecular weight 450.3Da
Lipinski: ≤ 500 Da
LogP (cLogP) 5.67
Lipinski: ≤ 5
Rotatable bonds 4

Conformational strain (MMFF94s)
Strain energy (ΔE) 16.28kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy 68.07kcal/mol
Minimised FF energy 51.78kcal/mol

SASA & burial

✓ computed
SASA (unbound) 676.2Ų
Total solvent-accessible surface area of free ligand
BSA total 531.1Ų
Buried surface area upon binding
BSA apolar 393.5Ų
Hydrophobic contacts buried
BSA polar 137.6Ų
Polar contacts buried
Fraction buried 78.5%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 74.1%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -2465.6Ų
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 1404.0Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)