FAIRMol

Z18809786

Pose ID 2704 Compound 1860 Pose 671

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
T04
L. major PTR1 L. major
Ligand Z18809786
PDB7PXX↗

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 medium Native mixed SASA done
Strain ΔE
40.0 kcal/mol
Protein clashes
3
Internal clashes
5
Native overlap
contact recall 0.53, Jaccard 0.50, H-bond role recall 0.20
Burial
77%
Hydrophobic fit
84%
Reason: no major geometry red flags detected
3 protein-contact clashes 5 intramolecular clashes
Molecular report
Full metrics ↗
Weak Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-0.701 kcal/mol/HA) ✓ Good fit quality (FQ -6.90) ✓ Deep burial (77% SASA buried) ✓ Lipophilic contacts well-matched (84%) ✗ Very high strain energy (40.0 kcal/mol) ✗ Geometry warnings ✗ Minor protein-contact clashes (4) ✗ Many internal clashes (19)
Score
-22.445
kcal/mol
LE
-0.701
kcal/mol/HA
Fit Quality
-6.90
FQ (Leeson)
HAC
32
heavy atoms
MW
429
Da
LogP
4.84
cLogP
Strain ΔE
40.0 kcal/mol
SASA buried
77%
Lipo contact
84% BSA apolar/total
SASA unbound
715 Ų
Apolar buried
461 Ų

Interaction summary

HB 1 HY 19 PI 4 CLASH 5

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
Final rank1.849Score-22.445
Inter norm-0.883Intra norm0.182
Top1000noExcludedno
Contacts11H-bonds1
Artifact reasongeometry warning; 19 clashes; 4 protein contact clashes; 2 cofactor-context clashes; high strain Δ 40.0
Residues
ARG17 HIS241 LEU188 LEU229 MET233 NDP302 PHE113 TYR191 TYR194 VAL237 ARG287

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 overlap10Native recall0.53
Jaccard0.50RMSD-
HB strict1Strict recall0.17
HB same residue+role1HB role recall0.20
HB same residue1HB residue recall0.20

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

All stored poses for this docking hit

PoseFinal rankInter normScoreHBCTCT overlapCT recallHB role rec.RMSDExcluded
652 1.6966319780527193 -0.810837 -29.5158 3 18 0 0.00 0.00 - no Open
671 1.8487580167981936 -0.883004 -22.4455 1 11 10 0.53 0.20 - no Current
674 4.407902746939831 -0.818431 -23.4464 7 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 -22.445kcal/mol
Ligand efficiency (LE) -0.7014kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -6.898
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 32HA

Physicochemical properties
Molecular weight 429.5Da
Lipinski: ≤ 500 Da
LogP (cLogP) 4.84
Lipinski: ≤ 5
Rotatable bonds 5

Conformational strain (MMFF94s)
Strain energy (ΔE) 39.97kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy 151.16kcal/mol
Minimised FF energy 111.19kcal/mol

SASA & burial

✓ computed
SASA (unbound) 714.8Ų
Total solvent-accessible surface area of free ligand
BSA total 549.2Ų
Buried surface area upon binding
BSA apolar 460.8Ų
Hydrophobic contacts buried
BSA polar 88.4Ų
Polar contacts buried
Fraction buried 76.8%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 83.9%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -1761.7Ų
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 1035.7Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)