FAIRMol

Z19674272

Pose ID 9356 Compound 3411 Pose 548

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 Z19674272
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 mixed SASA done
Strain ΔE
17.8 kcal/mol
Protein clashes
1
Internal clashes
1
Native overlap
contact recall 0.53, Jaccard 0.36, H-bond role recall 0.40
Burial
78%
Hydrophobic fit
80%
Reason: no major geometry red flags detected
1 protein-contact clashes 100% of hydrophobic surface is solvent-exposed (24/24 atoms). Large non-polar area without protein contacts incurs a desolvation penalty and will reduce binding affinity. Consider truncating or replacing the exposed fragment.
Molecular report
Full metrics ↗
Weak Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-0.603 kcal/mol/HA) ✓ Good fit quality (FQ -5.87) ✓ Good H-bonds (4 bonds) ✓ Deep burial (78% SASA buried) ✓ Lipophilic contacts well-matched (80%) ✗ Moderate strain (17.8 kcal/mol) ✗ Geometry warnings ✗ Many internal clashes (13)
Score
-18.690
kcal/mol
LE
-0.603
kcal/mol/HA
Fit Quality
-5.87
FQ (Leeson)
HAC
31
heavy atoms
MW
436
Da
LogP
4.36
cLogP
Final rank
2.4668
rank score
Inter norm
-0.747
normalised
Contacts
15
H-bonds 7
Strain ΔE
17.8 kcal/mol
SASA buried
78%
Lipo contact
80% BSA apolar/total
SASA unbound
685 Ų
Apolar buried
429 Ų

Interaction summary

HBD 1 HBA 3 HY 0 PI 0 CLASH 1

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
No hy · hydrophobic contacts detected for this pose.

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 overlap8Native recall0.53
Jaccard0.36RMSD-
HB strict1Strict recall0.17
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
570 2.2291047704872518 -0.81355 -11.9675 8 16 0 0.00 0.00 - no Open
547 2.386125910710143 -0.836388 -18.8413 11 15 0 0.00 0.00 - no Open
548 2.466779926075534 -0.747253 -18.69 7 15 8 0.53 0.40 - 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 -18.690kcal/mol
Ligand efficiency (LE) -0.6029kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -5.874
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 31HA

Physicochemical properties
Molecular weight 435.5Da
Lipinski: ≤ 500 Da
LogP (cLogP) 4.36
Lipinski: ≤ 5
Rotatable bonds 7

Conformational strain (MMFF94s)
Strain energy (ΔE) 17.85kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy 79.04kcal/mol
Minimised FF energy 61.20kcal/mol

SASA & burial

✓ computed
SASA (unbound) 685.4Ų
Total solvent-accessible surface area of free ligand
BSA total 535.4Ų
Buried surface area upon binding
BSA apolar 428.9Ų
Hydrophobic contacts buried
BSA polar 106.5Ų
Polar contacts buried
Fraction buried 78.1%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 80.1%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -2515.2Ų
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 1386.3Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)