FAIRMol

Z19278435

Pose ID 2490 Compound 496 Pose 457

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
T04
L. major PTR1 L. major
Ligand Z19278435
PDB7PXX↗

3D complex viewer

Strict H-bonds Permissive H-bonds
Viewer legend
Protein receptor
Pocket residues
Cofactor context
Docked ligand
Overall assessment
Reject SASA cached
Promising but geometrically suspicious
Binding strong Geometry low Native strong SASA done
Strain ΔE
42.5 kcal/mol
Protein clashes
0
Internal clashes
1
Native overlap
contact recall 0.68, Jaccard 0.59, H-bond role recall 0.40
Burial
75%
Hydrophobic fit
81%
Reason: strain 42.5 kcal/mol
strain ΔE 42.5 kcal/mol
Molecular report
Full metrics ↗
Reject Multiple quality flags — this pose should be deprioritised or discarded.
✓ Excellent LE (-0.838 kcal/mol/HA) ✓ Good fit quality (FQ -8.38) ✓ Deep burial (75% SASA buried) ✓ Lipophilic contacts well-matched (81%) ✗ Extreme strain energy (42.5 kcal/mol) ✗ Geometry warnings ✗ Many internal clashes (12)
Score
-28.484
kcal/mol
LE
-0.838
kcal/mol/HA
Fit Quality
-8.38
FQ (Leeson)
HAC
34
heavy atoms
MW
484
Da
LogP
2.26
cLogP
Strain ΔE
42.5 kcal/mol
SASA buried
75%
Lipo contact
81% BSA apolar/total
SASA unbound
752 Ų
Apolar buried
457 Ų

Interaction summary

HB 2 HY 21 PI 4 CLASH 1
Final rank3.067Score-28.484
Inter norm-0.763Intra norm-0.075
Top1000noExcludedno
Contacts16H-bonds2
Artifact reasongeometry warning; 12 clashes; 2 protein clashes; 1 cofactor-context clash; high strain Δ 40.2
Residues
ARG17 GLY225 HIS241 LEU188 LEU226 LEU229 LYS244 NDP302 PHE113 PRO115 SER227 TYR191 TYR194 TYR283 ALA288 ARG287

Protein summary

308 residues
Protein targetT04Atoms4210
Residues308Chains3
Residue summaryLEU:494; ALA:421; ARG:384; VAL:368; THR:295; TYR:231; SER:198; PRO:196; ILE:190; LYS:176; ASN:154; GLU:150; GLY:126; PHE:120; HIS:119; ASP:108

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:NDP302

Native ligand reference

★ reference
Interaction fingerprint calculated directly from the uploaded native ligand without docking. Current H-bond mode: strict.
Name7PXXContacts19
PoseOpen native poseHB0
IFP residues
ARG17 ASP181 GLY225 HIS241 LEU188 LEU226 LEU229 LYS198 MET233 NDP302 PHE113 PRO115 SER111 SER112 SER227 TYR191 TYR194 VAL230 ARG287
Current overlap13Native recall0.68
Jaccard0.59RMSD-
HB strict2Strict recall0.33
HB same residue+role2HB role recall0.40
HB same residue2HB residue recall0.40

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

PI · π–π interactions
Native π–π recall is disabled because no explicit native π–π reference was stored.

HY · Hydrophobic contacts

CLASH · Clashes

All stored poses for this docking hit

PoseFinal rankInter normScoreHBCTCT overlapCT recallHB role rec.RMSDExcluded
484 2.1524713220498173 -0.79102 -20.4726 4 16 0 0.00 0.00 - no Open
512 2.8158595554520227 -0.75712 -27.6762 3 18 0 0.00 0.00 - no Open
457 3.066687723246015 -0.762918 -28.4843 2 16 13 0.68 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 -28.484kcal/mol
Ligand efficiency (LE) -0.8378kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -8.383
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 34HA

Physicochemical properties
Molecular weight 483.6Da
Lipinski: ≤ 500 Da
LogP (cLogP) 2.26
Lipinski: ≤ 5
Rotatable bonds 8

Conformational strain (MMFF94s)
Strain energy (ΔE) 42.54kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy 63.74kcal/mol
Minimised FF energy 21.20kcal/mol

SASA & burial

✓ computed
SASA (unbound) 752.3Ų
Total solvent-accessible surface area of free ligand
BSA total 562.9Ų
Buried surface area upon binding
BSA apolar 457.5Ų
Hydrophobic contacts buried
BSA polar 105.4Ų
Polar contacts buried
Fraction buried 74.8%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 81.3%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -1762.3Ų
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 2179.4Ų
Non-polar SASA of receptor alone (VdW proxy, nonpolar atoms only)
Complex non-polar SASA 1030.5Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)