FAIRMol

Z167105928

Pose ID 9280 Compound 2321 Pose 472

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 Z167105928
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
28.5 kcal/mol
Protein clashes
2
Internal clashes
2
Native overlap
contact recall 0.47, Jaccard 0.32, H-bond role recall 0.20
Burial
80%
Hydrophobic fit
79%
Reason: no major geometry red flags detected
2 protein-contact clashes 50% of hydrophobic surface appears solvent-exposed (9/18 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 (-0.904 kcal/mol/HA) ✓ Good fit quality (FQ -8.22) ✓ Good H-bonds (5 bonds) ✓ Deep burial (80% SASA buried) ✓ Lipophilic contacts well-matched (79%) ✗ High strain energy (28.5 kcal/mol) ✗ Geometry warnings ✗ Internal clashes (6)
Score
-22.599
kcal/mol
LE
-0.904
kcal/mol/HA
Fit Quality
-8.22
FQ (Leeson)
HAC
25
heavy atoms
MW
353
Da
LogP
3.06
cLogP
Strain ΔE
28.5 kcal/mol
SASA buried
80%
Lipo contact
79% BSA apolar/total
SASA unbound
611 Ų
Apolar buried
389 Ų

Interaction summary

HB 5 HY 8 PI 0 CLASH 2 ⚠ Exposure 50%
⚠️Partial hydrophobic solvent exposure
50% of hydrophobic surface appears solvent-exposed (9/18 atoms). Partial exposure is common but may limit selectivity and membrane permeability.
Non-polar atoms 18 Buried (contacted) 9 Exposed 9 LogP 3.06 H-bonds 5
Exposed fragments: phenyl (2/5 atoms exposed)phenyl (6/7 atoms exposed)aliphatic chain/group (2 atoms exposed)
Final rank1.899Score-22.599
Inter norm-0.944Intra norm0.039
Top1000noExcludedno
Contacts14H-bonds5
Artifact reasongeometry warning; 6 clashes; 1 protein clash; moderate strain Δ 28.5
Residues
ARG22 ARG342 ARG50 ASN20 ASP44 CYS26 GLN341 GLU343 GLU384 LEU25 LEU382 PRO344 THR21 THR285

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

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
Jaccard0.32RMSD-
HB strict1Strict recall0.17
HB same residue+role1HB role recall0.20
HB same residue1HB residue recall0.20

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

All stored poses for this docking hit

PoseFinal rankInter normScoreHBCTCT overlapCT recallHB role rec.RMSDExcluded
86 -0.4618100082183587 -0.957775 -18.2786 1 16 0 0.00 0.00 - no Open
456 -0.30632342824977743 -0.95427 -17.506 1 16 0 0.00 0.00 - no Open
472 1.8985499783618167 -0.944176 -22.5995 5 14 7 0.47 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 -22.599kcal/mol
Ligand efficiency (LE) -0.9040kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -8.218
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 25HA

Physicochemical properties
Molecular weight 353.4Da
Lipinski: ≤ 500 Da
LogP (cLogP) 3.06
Lipinski: ≤ 5
Rotatable bonds 4

Conformational strain (MMFF94s)
Strain energy (ΔE) 28.52kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy 40.56kcal/mol
Minimised FF energy 12.05kcal/mol

SASA & burial

✓ computed
SASA (unbound) 610.8Ų
Total solvent-accessible surface area of free ligand
BSA total 491.0Ų
Buried surface area upon binding
BSA apolar 389.1Ų
Hydrophobic contacts buried
BSA polar 101.9Ų
Polar contacts buried
Fraction buried 80.4%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 79.2%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -2469.2Ų
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 1369.0Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)