FAIRMol

Z1537384907

Pose ID 3223 Compound 2095 Pose 513

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
T05
L. major PTR1 L. major
Ligand Z1537384907
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 high Native strong SASA done
Strain ΔE
11.3 kcal/mol
Protein clashes
2
Internal clashes
2
Native overlap
contact recall 0.59, Jaccard 0.53, H-bond role recall 0.17
Burial
87%
Hydrophobic fit
91%
Reason: no major geometry red flags detected
2 protein-contact clashes
Molecular report
Full metrics ↗
Weak Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-0.994 kcal/mol/HA) ✓ Good fit quality (FQ -9.15) ✓ Deep burial (87% SASA buried) ✓ Lipophilic contacts well-matched (91%) ✗ Moderate strain (11.3 kcal/mol) ✗ Geometry warnings ✗ Many internal clashes (12)
Score
-25.830
kcal/mol
LE
-0.994
kcal/mol/HA
Fit Quality
-9.15
FQ (Leeson)
HAC
26
heavy atoms
MW
344
Da
LogP
4.36
cLogP
Strain ΔE
11.3 kcal/mol
SASA buried
87%
Lipo contact
91% BSA apolar/total
SASA unbound
626 Ų
Apolar buried
491 Ų

Interaction summary

HB 2 HY 18 PI 3 CLASH 2

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 rank1.781Score-25.830
Inter norm-1.133Intra norm0.140
Top1000noExcludedno
Contacts12H-bonds2
Artifact reasongeometry warning; 12 clashes; 1 protein clash; 1 cofactor-context clash
Residues
ARG17 ASP181 HIS241 LEU188 LEU226 NDP302 PHE113 SER111 SER112 TYR194 VAL230 ARG287

Native ligand reference

★ reference
Interaction fingerprint calculated directly from the uploaded native ligand without docking. Current H-bond mode: strict.
NameligandContacts17
PoseOpen native poseHB0
IFP residues
ARG17 GLY225 HIS241 LEU188 LEU226 LEU229 LYS198 MET233 NDP302 PHE113 PRO115 SER111 SER227 TYR191 TYR194 VAL230 ARG287
Current overlap10Native recall0.59
Jaccard0.53RMSD-
HB strict1Strict recall0.14
HB same residue+role1HB role recall0.17
HB same residue1HB residue recall0.20

Protein summary

274 residues
Protein targetT05Atoms4108
Residues274Chains2
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
524 0.5905835506967564 -0.910304 -24.2391 1 17 0 0.00 0.00 - no Open
513 1.7811485430227114 -1.13322 -25.8302 2 12 10 0.59 0.17 - no Current
538 1.9087060180372954 -1.2628 -31.6204 6 19 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 -25.830kcal/mol
Ligand efficiency (LE) -0.9935kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -9.153
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 26HA

Physicochemical properties
Molecular weight 344.4Da
Lipinski: ≤ 500 Da
LogP (cLogP) 4.36
Lipinski: ≤ 5
Rotatable bonds 5

Conformational strain (MMFF94s)
Strain energy (ΔE) 11.29kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy 53.10kcal/mol
Minimised FF energy 41.81kcal/mol

SASA & burial

✓ computed
SASA (unbound) 625.5Ų
Total solvent-accessible surface area of free ligand
BSA total 541.8Ų
Buried surface area upon binding
BSA apolar 491.4Ų
Hydrophobic contacts buried
BSA polar 50.4Ų
Polar contacts buried
Fraction buried 86.6%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 90.7%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -1692.9Ų
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 1033.5Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)